RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-012 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:29:59 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_157 python-lpbuildd_157 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.3 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 8 Dec 17:07:14 ntpdate[1800]: adjust time server 10.211.37.1 offset 0.065004 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 /home/buildd/filecache-default/f027e517e95d0e91684230ee23be60d709f816c0 Creating target for build PACKAGEBUILD-13832550 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 Starting target for build PACKAGEBUILD-13832550 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-13832550 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 Updating target for build PACKAGEBUILD-13832550 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 Packages [1010 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe amd64 Packages [8339 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4897 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 Packages [60.6 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [28.4 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe amd64 Packages [180 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [98.1 kB] Fetched 15.6 MB in 4s (3569 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd binutils binutils-common binutils-x86-64-linux-gnu bsdutils build-essential coreutils cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libassuan0 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed4 libidn2-0 libip4tc0 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpx2 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support openssl optipng perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 103 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 62.2 MB of archives. After this operation, 785 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main amd64 base-files amd64 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main amd64 bsdutils amd64 1:2.30.2-0.1ubuntu1 [60.1 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main amd64 coreutils amd64 8.26-3ubuntu4 [1213 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main amd64 debianutils amd64 4.8.3 [85.8 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 dpkg amd64 1.19.0.4ubuntu1 [1145 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main amd64 libc6-dev amd64 2.26-0ubuntu2 [2524 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main amd64 libc-dev-bin amd64 2.26-0ubuntu2 [69.6 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 linux-libc-dev amd64 4.14.0-11.13 [960 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main amd64 libquadmath0 amd64 7.2.0-17ubuntu1 [133 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main amd64 libitm1 amd64 7.2.0-17ubuntu1 [27.6 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main amd64 gcc-7-base amd64 7.2.0-17ubuntu1 [18.8 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcc1 amd64 1:7.2.0-17ubuntu1 [39.3 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main amd64 libmpx2 amd64 7.2.0-17ubuntu1 [11.8 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main amd64 libgomp1 amd64 7.2.0-17ubuntu1 [76.3 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main amd64 libatomic1 amd64 7.2.0-17ubuntu1 [8988 B] Get:16 http://ftpmaster.internal/ubuntu bionic/main amd64 libasan4 amd64 7.2.0-17ubuntu1 [359 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main amd64 liblsan0 amd64 7.2.0-17ubuntu1 [134 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main amd64 libtsan0 amd64 7.2.0-17ubuntu1 [280 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main amd64 libubsan0 amd64 7.2.0-17ubuntu1 [126 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main amd64 libcilkrts5 amd64 7.2.0-17ubuntu1 [42.4 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main amd64 cpp-7 amd64 7.2.0-17ubuntu1 [6728 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main amd64 libcc1-0 amd64 7.2.0-17ubuntu1 [38.7 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main amd64 g++-7 amd64 7.2.0-17ubuntu1 [7549 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main amd64 gcc-7 amd64 7.2.0-17ubuntu1 [7419 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcc-7-dev amd64 7.2.0-17ubuntu1 [2378 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main amd64 libstdc++-7-dev amd64 7.2.0-17ubuntu1 [1455 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main amd64 libstdc++6 amd64 7.2.0-17ubuntu1 [397 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1.1 [241 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main amd64 libbinutils amd64 2.29.1-10ubuntu1 [503 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils amd64 2.29.1-10ubuntu1 [3412 B] Get:31 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils-common amd64 2.29.1-10ubuntu1 [190 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main amd64 binutils-x86-64-linux-gnu amd64 2.29.1-10ubuntu1 [1824 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main amd64 libc6 amd64 2.26-0ubuntu2 [2778 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main amd64 e2fslibs amd64 1.43.7-1 [157 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main amd64 e2fsprogs amd64 1.43.7-1 [498 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main amd64 findutils amd64 4.6.0+git+20170828-2 [291 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main amd64 perl-modules-5.26 all 5.26.1-3 [2761 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main amd64 libperl5.26 amd64 5.26.1-3 [3541 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main amd64 perl amd64 5.26.1-3 [201 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main amd64 perl-base amd64 5.26.1-3 [1389 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main amd64 libuuid1 amd64 2.30.2-0.1ubuntu1 [14.8 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main amd64 libblkid1 amd64 2.30.2-0.1ubuntu1 [119 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main amd64 libsmartcols1 amd64 2.30.2-0.1ubuntu1 [78.8 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main amd64 libfdisk1 amd64 2.30.2-0.1ubuntu1 [157 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main amd64 libpcre3 amd64 2:8.39-8 [229 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main amd64 libselinux1 amd64 2.7-2 [68.3 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main amd64 libmount1 amd64 2.30.2-0.1ubuntu1 [131 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main amd64 fdisk amd64 2.30.2-0.1ubuntu1 [105 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main amd64 util-linux amd64 2.30.2-0.1ubuntu1 [879 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main amd64 base-passwd amd64 3.5.44 [47.2 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main amd64 libc-bin amd64 2.26-0ubuntu2 [593 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main amd64 sysvinit-utils amd64 2.88dsf-59.10ubuntu1 [18.6 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main amd64 libudev1 amd64 235-3ubuntu2 [54.8 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main amd64 libapt-pkg5.0 amd64 1.6~alpha5 [778 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main amd64 debconf all 1.5.65 [124 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 adduser all 3.116ubuntu1 [163 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main amd64 libgpg-error0 amd64 1.27-5 [36.9 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main amd64 libgcrypt20 amd64 1.8.1-4 [417 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main amd64 gpgv amd64 2.1.15-1ubuntu8 [186 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main amd64 libseccomp2 amd64 2.3.1-2.1ubuntu3 [37.3 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main amd64 apt amd64 1.6~alpha5 [1145 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main amd64 libapparmor1 amd64 2.11.0-2ubuntu18 [28.8 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main amd64 libcap2 amd64 1:2.25-1.2 [13.0 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main amd64 libip4tc0 amd64 1.6.1-2ubuntu2 [19.6 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main amd64 mount amd64 2.30.2-0.1ubuntu1 [110 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main amd64 systemd amd64 235-3ubuntu2 [2834 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main amd64 libsystemd0 amd64 235-3ubuntu2 [196 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main amd64 systemd-sysv amd64 235-3ubuntu2 [13.1 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main amd64 libcap-ng0 amd64 0.7.7-3.1 [11.1 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main amd64 libcomerr2 amd64 1.43.7-1 [11.4 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage-common all 2.7-2 [6916 B] Get:72 http://ftpmaster.internal/ubuntu bionic/main amd64 libsemanage1 amd64 2.7-2 [84.6 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main amd64 libss2 amd64 1.43.7-1 [11.1 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main amd64 libnettle6 amd64 3.3-2 [91.7 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main amd64 libhogweed4 amd64 3.3-2 [135 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main amd64 libp11-kit0 amd64 0.23.9-2 [187 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main amd64 libtasn1-6 amd64 4.12-3 [36.1 kB] Get:78 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main amd64 sensible-utils all 0.0.11 [14.8 kB] Get:80 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libassuan0 amd64 2.4.5-1 [34.8 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main amd64 pinentry-curses amd64 1.0.0-3 [34.7 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main amd64 libnpth0 amd64 1.5-3 [7668 B] Get:83 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg amd64 2.1.15-1ubuntu8 [780 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main amd64 gnupg-agent amd64 2.1.15-1ubuntu8 [255 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main amd64 libsqlite3-0 amd64 3.21.0-1 [492 kB] Get:86 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libssl1.0.0 amd64 1.0.2g-1ubuntu15 [1080 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main amd64 multiarch-support amd64 2.26-0ubuntu2 [6832 B] Get:88 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 openssl amd64 1.0.2g-1ubuntu15 [495 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main amd64 tzdata all 2017c-1 [188 kB] Get:90 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libgssapi-krb5-2 amd64 1.15.2-2 [121 kB] Get:91 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libkrb5-3 amd64 1.15.2-2 [278 kB] Get:92 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libkrb5support0 amd64 1.15.2-2 [31.5 kB] Get:93 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libk5crypto3 amd64 1.15.2-2 [85.4 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main amd64 libkeyutils1 amd64 1.5.9-9.2ubuntu1 [9308 B] Get:95 http://ftpmaster.internal/ubuntu bionic/main amd64 libidn2-0 amd64 2.0.4-1 [93.2 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main amd64 libpng16-16 amd64 1.6.34-1 [176 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/universe amd64 apt-transport-https all 1.6~alpha5 [1692 B] Get:98 http://ftpmaster.internal/ubuntu bionic/main amd64 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/main amd64 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:100 http://ftpmaster.internal/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4758 B] Get:101 http://ftpmaster.internal/ubuntu bionic/main amd64 libpsl5 amd64 0.19.1-4 [41.2 kB] Get:102 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libcurl3-gnutls amd64 7.55.1-1ubuntu3 [193 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main amd64 optipng amd64 0.7.6-1ubuntu1 [83.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.2 MB in 7s (8676 kB/s) (Reading database ... 12676 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_amd64.deb ... Unpacking base-files (10ubuntu1) over (9.6ubuntu101) ... Setting up base-files (10ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12676 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.2-0.1ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.30.2-0.1ubuntu1) over (1:2.30.1-0ubuntu4) ... Setting up bsdutils (1:2.30.2-0.1ubuntu1) ... (Reading database ... 12676 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_amd64.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12676 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13832550 amd64 bionic-proposed -c chroot:build-PACKAGEBUILD-13832550 --arch=amd64 --dist=bionic-proposed --nolog -A plink_1.07+dfsg-1.dsc Initiating build PACKAGEBUILD-13832550 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:29:59 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-012.buildd +==============================================================================+ | plink 1.07+dfsg-1 (amd64) 08 Dec 2017 17:08 | +==============================================================================+ Package: plink Version: 1.07+dfsg-1 Source Version: 1.07+dfsg-1 Distribution: bionic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/plink-LnOnj5/plink-1.07+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/plink-LnOnj5' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13832550/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- plink_1.07+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-8onAc7/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-8onAc7/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8onAc7/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8onAc7/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8onAc7/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-8onAc7/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (29.9 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 libwind0-heimdal Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-8onAc7/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12679 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), zlib1g-dev Filtered Build-Depends: debhelper (>= 10), zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-plink-dummy' in '/<>/resolver-2lDTRJ/apt_archive/sbuild-build-depends-plink-dummy.deb'. Ign:1 copy:/<>/resolver-2lDTRJ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2lDTRJ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-2lDTRJ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2lDTRJ/apt_archive ./ Sources [215 B] Get:5 copy:/<>/resolver-2lDTRJ/apt_archive ./ Packages [535 B] Fetched 2869 B in 0s (52.4 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install plink build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libustr-1.0-1 libwind0-heimdal Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-plink-dummy zlib1g-dev 0 upgraded, 31 newly installed, 1 to remove and 0 not upgraded. Need to get 16.8 MB of archives. After this operation, 62.9 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2lDTRJ/apt_archive ./ sbuild-build-depends-plink-dummy 0.invalid.0 [864 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main amd64 groff-base amd64 1.22.3-9 [1144 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main amd64 libbsd0 amd64 0.8.6-3 [41.7 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main amd64 bsdmainutils amd64 9.0.14ubuntu1 [179 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main amd64 man-db amd64 2.7.6.1-4 [898 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main amd64 libmagic-mgc amd64 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main amd64 libmagic1 amd64 1:5.32-1 [68.4 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main amd64 file amd64 1:5.32-1 [22.0 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main amd64 libglib2.0-0 amd64 2.54.1-1ubuntu1 [1163 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main amd64 libicu60 amd64 60.1-1ubuntu2 [8042 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/main amd64 libxml2 amd64 2.9.4+dfsg1-5.1ubuntu1 [669 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main amd64 gettext-base amd64 0.19.8.1-4ubuntu1 [49.4 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main amd64 libsigsegv2 amd64 2.11-1 [13.2 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main amd64 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main amd64 autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main amd64 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main amd64 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main amd64 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main amd64 dh-autoreconf all 15 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main amd64 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main amd64 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main amd64 libcroco3 amd64 0.6.12-1 [81.3 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main amd64 gettext amd64 0.19.8.1-4ubuntu1 [1093 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main amd64 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main amd64 debhelper all 10.10.9ubuntu1 [871 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.8 MB in 1s (15.5 MB/s) (Reading database ... 12679 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12670 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.6-3_amd64.deb ... Unpacking libbsd0:amd64 (0.8.6-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.14ubuntu1_amd64.deb ... Unpacking bsdmainutils (9.0.14ubuntu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-4_amd64.deb ... Unpacking man-db (2.7.6.1-4) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_amd64.deb ... 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Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package sbuild-build-depends-plink-dummy. Preparing to unpack .../30-sbuild-build-depends-plink-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-plink-dummy (0.invalid.0) ... Setting up libicu60:amd64 (60.1-1ubuntu2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:amd64 (0.8.6-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-5.1ubuntu1) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:amd64 (1:5.32-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20161112.1+nmu1) ... Setting up bsdmainutils (9.0.14ubuntu1) ... 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 autopoint (0.19.8.1-4ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (15) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up debhelper (10.10.9ubuntu1) ... Setting up sbuild-build-depends-plink-dummy (0.invalid.0) ... (Reading database ... 14513 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-101-generic amd64 (x86_64) Toolchain package versions: binutils_2.29.1-10ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-17ubuntu1 gcc-7_7.2.0-17ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-17ubuntu1 libstdc++6_7.2.0-17ubuntu1 linux-libc-dev_4.14.0-11.13 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 apt_1.6~alpha5 apt-transport-https_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1+nmu1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.1-10ubuntu1 binutils-common_2.29.1-10ubuntu1 binutils-x86-64-linux-gnu_2.29.1-10ubuntu1 bsdmainutils_9.0.14ubuntu1 bsdutils_1:2.30.2-0.1ubuntu1 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3ubuntu4 cpp_4:7.2.0-1ubuntu1 cpp-7_7.2.0-17ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.65 debhelper_10.10.9ubuntu1 debianutils_4.8.3 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.19.0.4ubuntu1 dpkg-dev_1.19.0.4ubuntu1 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.2-0.1ubuntu1 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1ubuntu1 g++-7_7.2.0-17ubuntu1 gcc_4:7.2.0-1ubuntu1 gcc-7_7.2.0-17ubuntu1 gcc-7-base_7.2.0-17ubuntu1 gettext_0.19.8.1-4ubuntu1 gettext-base_0.19.8.1-4ubuntu1 gnupg_2.1.15-1ubuntu8 gnupg-agent_2.1.15-1ubuntu8 gpgv_2.1.15-1ubuntu8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49ubuntu1 init-system-helpers_1.49ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu18 libapt-pkg5.0_1.6~alpha5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-17ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.5-1 libatomic1_7.2.0-17ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libbinutils_2.29.1-10ubuntu1 libblkid1_2.30.2-0.1ubuntu1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-0ubuntu2 libc-dev-bin_2.26-0ubuntu2 libc6_2.26-0ubuntu2 libc6-dev_2.26-0ubuntu2 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_7.2.0-17ubuntu1 libcilkrts5_7.2.0-17ubuntu1 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3-gnutls_7.55.1-1ubuntu3 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu3 libdpkg-perl_1.19.0.4ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.2-0.1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-17ubuntu1 libgcc1_1:7.2.0-17ubuntu1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1ubuntu1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-17ubuntu1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.15.2-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-2 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu60_60.1-1ubuntu2 libidn11_1.33-2 libidn2-0_2.0.4-1 libip4tc0_1.6.1-2ubuntu2 libisl15_0.18-1 libitm1_7.2.0-17ubuntu1 libk5crypto3_1.15.2-2 libkeyutils1_1.5.9-9.2ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.2-2 libkrb5support0_1.15.2-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.2.0-17ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1ubuntu1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libmpx2_7.2.0-17ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-2 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-8 libperl5.26_5.26.1-3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.19.1-4 libquadmath0_7.2.0-17ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu3 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.2-0.1ubuntu1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.0.0_1.0.2g-1ubuntu15 libstdc++-7-dev_7.2.0-17ubuntu1 libstdc++6_7.2.0-17ubuntu1 libsystemd0_235-3ubuntu2 libtasn1-6_4.12-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.2.0-17ubuntu1 libubsan0_7.2.0-17ubuntu1 libudev1_235-3ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1ubuntu1 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-5.1ubuntu1 linux-libc-dev_4.14.0-11.13 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-4 mawk_1.3.3-17ubuntu2 mount_2.30.2-0.1ubuntu1 multiarch-support_2.26-0ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu15 optipng_0.7.6-1ubuntu1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.1-3 perl-base_5.26.1-3 perl-modules-5.26_5.26.1-3 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-plink-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-3ubuntu2 systemd-sysv_235-3ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.2-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Dec 8 10:29:15 2017 UTC gpgv: using RSA key gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plink_1.07+dfsg-1.dsc dpkg-source: info: extracting plink in plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-1.debian.tar.xz dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13832550 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13832550 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13832550 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build plink-1.07+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/plink-1.07+dfsg' dh_auto_clean make -j4 clean make[2]: Entering directory '/<>/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/<>/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/<>/plink-1.07+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>/plink-1.07+dfsg' /usr/bin/make CXXFLAGS='-Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make[2]: Entering directory '/<>/plink-1.07+dfsg' g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp In file included from plink.cpp:28:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp In file included from options.cpp:16:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp In file included from input.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:516:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i == include.size() ) ~~^~~~~~~~~~~~~~~~~ input.cpp:521:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&, int&)’: input.cpp:2116:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp In file included from binput.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function ‘void Plink::readBinData()’: binput.cpp:126:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp In file included from tinput.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function ‘void Plink::readTransposedData()’: tinput.cpp:161:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i sample.size()) ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * sample.size() ) ~~~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp In file included from genome.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:1227:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp In file included from helper.h:24:0, from helper.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function ‘std::__cxx11::string display(std::vector >&)’: helper.cpp:58:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&)’: helper.cpp:66:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)’: helper.cpp:100:18: 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::__cxx11::string)’: helper.cpp:193:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int t=0; t > CArgs::value(std::__cxx11::string, int)’: helper.cpp:267:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( (i+j) < a.size() ) ~~~~~~^~~~~~~~~~ helper.cpp:277:16: 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::__cxx11::string)’: helper.cpp:306:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0 ; i < s.length() ; i++) ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (s[i] == ',' || i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ helper.cpp:309:8: 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::__cxx11::string)’: helper.cpp:323:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i > listPossibleHaplotypes(Plink&, std::vector)’: helper.cpp:709:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(h&, matrix_t&, boolmatrix_t&, bool)’: helper.cpp:795:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s = 0 ; s < snps.size() ; s++) ~~^~~~~~~~~~~~~ helper.cpp: In function ‘std::__cxx11::string chromosomeName(int)’: helper.cpp:952:19: 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::__cxx11::string)’: helper.cpp:959:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i getChromosomeMarkerRange(Plink&, int)’: helper.cpp:989:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i getChromosomeRange(Plink&)’: helper.cpp:1040:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i >)’: helper.cpp:1172:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kfid.length() > par::pp_maxfid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1267:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (sample[i]->iid.length() > par::pp_maxiid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1273:33: 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:1389:19: 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:2455:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i, Individual*>&)’: helper.cpp:2935:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)’: helper.cpp:2959:21: 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::__cxx11::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::__cxx11::string CArgs::value(std::__cxx11::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::__cxx11::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::__cxx11::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::__cxx11::string)’: helper.cpp:256:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ helper.cpp: In function ‘int getInt(std::__cxx11::string, std::__cxx11::string)’: helper.cpp:380:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ helper.cpp: In function ‘long unsigned int getLongUnsignedInt(std::__cxx11::string, std::__cxx11::string)’: helper.cpp:393:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ helper.cpp: In function ‘double getDouble(std::__cxx11::string, std::__cxx11::string)’: helper.cpp:407:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ helper.cpp: In function ‘std::vector vif_prune(std::vector >, double, std::vector&)’: helper.cpp:1430:12: warning: ‘maxI’ may be used uninitialized in this function [-Wmaybe-uninitialized] cur[maxI] = false; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:1477:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1521:22: 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:1531:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < v.size(); i++) ~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp In file included from filters.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:95:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp In file included from locus.cpp:16:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp In file included from multi.cpp:16:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:295:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from helper.h:24:0, from cluster.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function ‘void Plink::buildCluster()’: cluster.cpp:272:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=1; z<=qt.size(); z++) ~^~~~~~~~~~~ cluster.cpp:452:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;i >&, std::vector&, std::vector&)’: cluster.cpp:1203:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)’: cluster.cpp:1228:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&)’: cluster.cpp:1254:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&)’: cluster.cpp:1272:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)’: cluster.cpp:1290:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from mds.cpp:21:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function ‘void Plink::generateMDS()’: mds.cpp:190:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i1=0; i1>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp In file included from output.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function ‘void Plink::displayGenomePV()’: output.cpp:84:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i::iterator loc1 = locus.begin()+m1; ^~~~ output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable] vector::iterator loc2 = locus.begin()+m2; ^~~~ output.cpp: In member function ‘void Plink::extractExcludeSet(bool)’: output.cpp:520:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp In file included from informative.cpp:18:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function ‘int Plink::readInformative()’: informative.cpp:80:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 4; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp In file included from helper.h:24:0, from assoc.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from assoc.cpp:29:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:18: 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 ‘std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)’: assoc.cpp:1108:4: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized] if ( pvalue <= par::set_score_p && pvalue >= 0 ) ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp In file included from epi.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:146:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int e=0;e>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In file included from prephap.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp In file included from phase.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27:0: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)’: phase.cpp:472:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (h&)’: phase.cpp:1888:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0; z < h1.size(); z++) ~~^~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp In file included from trio.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:91:18: 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:258:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:272:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:335:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp:350:24: 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:469:18: 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:1038:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fpm->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; kpp->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from tdt.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:81:19: 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:132:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); c++) ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:18: 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:522:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp In file included from perm.h:17:0, from sharing.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function ‘void Plink::perm_sharingIBSTest(Perm&)’: sharing.cpp:102:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp In file included from genepi.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.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:334:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s >&, Set&, Plink&)’: genepi.cpp:489:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l >&, Set&, Plink&)’: genepi.cpp:1025:21: 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:805:82: warning: ‘cancor1_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized] gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp In file included from sets.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:41: 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:99:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp In file included from perm.h:17:0, from perm.cpp:17: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function ‘void Perm::permuteInCluster()’: perm.cpp:144:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j&, std::vector&)’: perm.cpp:273:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0;j< P.pS->snpset[l].size();j++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:747:18: 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:1249:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp In file included from perm.h:17:0, from genedrop.cpp:17: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function ‘void Perm::preGeneDrop()’: genedrop.cpp:64:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, std::vector&, std::vector&, std::map&)’: genedrop.cpp:340:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kkids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from merge.cpp:22:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:333:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i include.size()) ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp In file included from hotel.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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’ [-Wdangling-else] if (!sample[i]->missing) ^ hotel.cpp:173:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp In file included from helper.h:24:0, from multiple.cpp:22: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function ‘void Plink::multcomp(std::vector&, std::__cxx11::string)’: multiple.cpp:85:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp In file included from haploCC.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, int, bool)’: haploCC.cpp:48:27: 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:79:27: 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:340:28: 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:375:28: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from haploTDT.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp In file included from poo.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function ‘void Plink::perm_testTDT_POO(Perm&)’: poo.cpp:93:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fpv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:18: 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:293:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp In file included from helper.h:24:0, from webcheck.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function ‘void Plink::webcheck(CArgs&)’: webcheck.cpp:117:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp In file included from helper.h:24:0, from qfam.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function ‘void scoreBetween(Plink&, int)’: qfam.cpp:82:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:24: 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:267:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < family.size(); i++) ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: 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:505:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < (*f)->kid.size() ; k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp In file included from helper.h:24:0, from linear.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function ‘virtual void LinearModel::pruneY()’: linear.cpp:50:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp In file included from bmerge.cpp:22:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.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:357:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isecond; ^~~~ bmerge.cpp:697:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp In file included from parse.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp In file included from mishap.cpp:17:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; ihap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:368:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp In file included from helper.h:24:0, from homozyg.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function ‘void displayPoolVerbose(Plink&, Pool*, std::ofstream&)’: homozyg.cpp:673:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:756:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:861:20: 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:1134:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1178:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1331:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< (*pA)->segs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( (*pA)->match[i].size() >= maxlist ) ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:20: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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::segmentPermutationTest(Perm&, bool, std::__cxx11::string, std::vector&, std::vector&, std::vector&)’: segment.cpp:871:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (!ibd) ^~ segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ SIBS << setw(10) << original[l] << " " ^~~~ 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:1529:17: 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:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp In file included from model.cpp:15:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&)’: model.cpp:132:23: 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:354:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< par::parameter_list.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0 ; i < X.size() ; i++) ~~^~~~~~~~~~ model.cpp:374:24: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:66:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp In file included from helper.h:24:0, from glm.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from glm.cpp:25:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; icurrent->group.size(); h++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; c>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp dcdflib.cpp: In function ‘void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)’: dcdflib.cpp:1882:36: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] if(!(*s < 0.0e0 || *which != 3 && *s > *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: ISO C++ forbids converting a 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: ISO C++ forbids converting a 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: ISO C++ forbids converting a 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:493:27: 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:609:18: 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:895:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++) ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: 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:374:10: warning: ‘wt’ may be used uninitialized in this function [-Wmaybe-uninitialized] double wt; ^~ elf.cpp: In member function ‘void Plink::elfBaseline()’: elf.cpp:1154:8: warning: ‘p_gcnt’ may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_gcnt); ^~~~~~~~~~~ elf.cpp:1165:5: warning: ‘p_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_cnt); ^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp In file included from dfam.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:76:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:106:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; fkid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:23: 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:504:21: 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; ^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: ISO C++ forbids converting a 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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:449:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (*ncol <= 1) ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ for (i = 1; i <= *ldkey << 1; ++i) { ^~~ fisher.cpp:501:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: ISO C++ forbids converting a 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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: ISO C++ forbids converting a 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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function ‘void isort(int*, int*)’: fisher.cpp:2078:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] prterr(20, "This should never occur."); ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp In file included from linput.cpp:25:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:68:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp In file included from helper.h:24:0, from sockets.cpp:18: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function ‘std::vector > socketConnection(Plink*, std::__cxx11::string, int, std::__cxx11::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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:206:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=25; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp In file included from proxy.cpp:21:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i= par::proxy_snp_filter ) ~~~~~~~~~~~~~^~~~~~ proxy.cpp:854:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: 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:939:58: warning: ‘ref’ may be used uninitialized in this function [-Wmaybe-uninitialized] haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " "; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp In file included from pdriver.cpp:16:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from haploQTL.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploQTL.cpp:25:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i&, int, bool)’: haploQTL.cpp:83:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from haplohelper.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i > HaploPhase::returnHaplotypes(std::vector&)’: haplohelper.cpp:297:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int h=0; h&)’: haplohelper.cpp:1419:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:23: 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:1666:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z = 0; z < windows[w]->hap1[r].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplowindow.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: 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:183:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (h>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from genogroup.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp In file included from nonfounderphasing.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27:0: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i clump_LD::read_assoc_file(std::__cxx11::string)’: clumpld.cpp:92:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; flocus.size()-1 ) ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( j < grouped_snps.size()-1) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from genoerr.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp In file included from em.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from em.cpp:27:0: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp In file included from impute.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:27:0: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; ihap1[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:23: 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:263:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s < g.size(); s++) ~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp In file included from metaem.cpp:24:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp In file included from profile.cpp:23:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.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:390:22: 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:629:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j&, std::map >&, std::map&, std::ofstream&)’: profile.cpp:667:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp In file included from helper.h:24:0, from nlist.h:21, from nlist.cpp:17: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function ‘std::vector NList::deparseNumberList(std::__cxx11::string)’: nlist.cpp:38:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i NList::deparseStringList(std::__cxx11::string, std::map, int>*)’: nlist.cpp:83:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i NList::expandNumberList(std::vector&)’: nlist.cpp:107:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i > NList::tokenize(std::__cxx11::string)’: nlist.cpp:189:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp In file included from helper.h:24:0, from whap.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25:0: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; ins + H->nh ) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i< lst.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1142:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; iconditioner.size(); c++) ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l&, ChapModel&)’: whap.cpp:1389:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0;l0 && cnt2 < m.group[h].size() ) ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:635:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s=0; s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24:0, from gvar.cpp:15: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function ‘void Plink::readGenericVariantData()’: gvar.cpp:125:22: 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:549:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp In file included from helper.h:24:0, from cnv.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.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:678:36: warning: variable ‘is’ set but not used [-Wunused-but-set-variable] map::iterator is = idescription.find(*ir); ^~ cnv.cpp:815:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s1=0; s1::iterator i2 = isection.begin(); ^~ cnv.cpp:1103:36: warning: variable ‘il’ set but not used [-Wunused-but-set-variable] map::iterator il = segmentLength.find(t); ^~ cnv.cpp:1414:11: warning: unused variable ‘nseg’ [-Wunused-variable] int nseg = 1; ^~~~ cnv.cpp:412:7: warning: unused variable ‘nseg’ [-Wunused-variable] int nseg=0; ^~~~ cnv.cpp: In function ‘double weighted_count_intersects(std::set&, 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:2013:22: 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 ]; ^~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp In file included from greport.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:78:18: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from cfamily.cpp:18:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:205:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:221:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: 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:263:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp In file included from setscreen.cpp:21:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:80:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; isnpset.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < snpset[j].size(); i++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp In file included from idhelp.cpp:18:0: idhelp.h: In member function ‘void IDGroup::display()’: idhelp.h:196:20: 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::__cxx11::string)’: idhelp.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:63:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i >&)’: idhelp.cpp:136:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int g=0; gvalues.size(); g++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: 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:210:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:24: 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:346:23: 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:502:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( p < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:547:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:553:24: 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:584:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:594:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:678:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:747:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:28: 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:772:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( tokens.size() != file->uniqFieldCount ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( j < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i=0; ivalue.size() + 3 > myField->width ) ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: 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:1025:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: 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:1070:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0; k < (*i0)->values.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=0; zvalues.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int z=0; z<(*i0)->values.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: 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:1346:22: 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:1551:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int i=0; ivalues.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i= tok.size() ) ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:19: 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:2167:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; kvalues.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from helper.h:24:0, from lookup2.cpp:18: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function ‘void Plink::lookup2()’: lookup2.cpp:163:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int t = 0 ; t < tokens.size() ; t++) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from blox.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: 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:418:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int k=0; k0 ) loglike1 += knownBA * log( pB1 ); ~~~^~~~~~~ blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized in this function [-Wmaybe-uninitialized] double pA = pA1 + pA2; ^~ blox.cpp:505:10: warning: ‘pA1’ may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp In file included from dosage.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:252:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; igetStatistic() : 0; ^~~~~~~~~ dosage.cpp:1252:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( o->second != dosageFilename_all.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:14: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from annot.cpp:20:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: 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:83:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=1; j>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp In file included from metaanal.cpp:21:0: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor ‘Alleles::Alleles(std::__cxx11::string, int, int, std::__cxx11::string, std::__cxx11::string)’: metaanal.cpp:47:7: warning: ‘Alleles::bp’ will be initialized after [-Wreorder] int bp; ^~ metaanal.cpp:44:10: warning: ‘std::__cxx11::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:159:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from helper.h:24:0, from r.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29:0: Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’: Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’: Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’: Rconnection.h:232:43: 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:245:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: 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 -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’: Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’: Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’: Rconnection.h:232:43: 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:245:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (i < nel) { ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor ‘virtual Rconnection::~Rconnection()’: Rconnection.cpp:567:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (host) free(host); host=0; ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (host) free(host); host=0; ^~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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 '/<>/plink-1.07+dfsg' make[1]: Leaving directory '/<>/plink-1.07+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/<>/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/<>/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/<>/plink-1.07+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing plink (in debian/plink); do_strip: , oemstrip: pkgstriptranslations: processing plink-dbgsym (in debian/.debhelper/plink/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/plink/DEBIAN/control, package plink, directory debian/plink .. removing usr/share/doc/plink/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/plink/dbgsym-root/DEBIAN/control, package plink-dbgsym, directory debian/.debhelper/plink/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package plink-dbgsym ... pkgstripfiles: No PNG files. pkgstripfiles: Truncating usr/share/doc/plink/changelog.Debian.gz to topmost ten records dpkg-deb: building package 'plink-dbgsym' in 'debian/.debhelper/scratch-space/build-plink/plink-dbgsym_1.07+dfsg-1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package plink ... pkgstripfiles: No PNG files. dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-1_amd64.deb'. Renaming plink-dbgsym_1.07+dfsg-1_amd64.deb to plink-dbgsym_1.07+dfsg-1_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../plink_1.07+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build plink-1.07+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171208-1716 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ plink_1.07+dfsg-1_amd64.changes: -------------------------------- Format: 1.8 Date: Fri, 08 Dec 2017 11:15:55 +0100 Source: plink Binary: plink Architecture: amd64 Version: 1.07+dfsg-1 Distribution: bionic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: plink - whole-genome association analysis toolset Closes: 883844 Changes: plink (1.07+dfsg-1) unstable; urgency=medium . * Properly repack source archive Closes: #883844 * Standards-Version: 4.1.2 Checksums-Sha1: 1b61c47b747b888f1946a1e6bbb5e420f590e1bd 18986420 plink-dbgsym_1.07+dfsg-1_amd64.ddeb 698cfcefcaa3d28504b859f2ebaf81be4e7b93d4 5021 plink_1.07+dfsg-1_amd64.buildinfo 49c440150de72d2e471bfd2f85084b6a60158163 1112320 plink_1.07+dfsg-1_amd64.deb Checksums-Sha256: 9b916c80ec4656dd224272a96f8d028f96ff3ee229fd52ecbfa5d5425369a493 18986420 plink-dbgsym_1.07+dfsg-1_amd64.ddeb e683ea5e4b773d8ec4cbb4b3d37175956a99c6daba92e0520b5f9d87c41200a5 5021 plink_1.07+dfsg-1_amd64.buildinfo 3a220b25c00b06b9eba930749e1c7a34f7b68a1dc49adbdafc0673e9c6f040f3 1112320 plink_1.07+dfsg-1_amd64.deb Files: a832d89ba3d878235ce2f2d491ee8d58 18986420 debug optional plink-dbgsym_1.07+dfsg-1_amd64.ddeb ee3807fbf0dae5296fed8ee8f7b06f39 5021 science optional plink_1.07+dfsg-1_amd64.buildinfo abcd4ffe387ccd9ac1f7e0d38a38f2d5 1112320 science optional plink_1.07+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ plink_1.07+dfsg-1_amd64.deb --------------------------- new debian package, version 2.0. size 1112320 bytes: control archive=1308 bytes. 1144 bytes, 27 lines control 848 bytes, 12 lines md5sums Package: plink Version: 1.07+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3157 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Recommends: med-config (>= 2.1) Section: science Priority: optional Homepage: http://zzz.bwh.harvard.edu/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 plink1 because of a name clash. Please read more about this in /usr/share/doc/README.Debian. drwxr-xr-x root/root 0 2017-12-08 10:15 ./ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/bin/ lrwxrwxrwx root/root 0 2017-12-08 10:15 ./usr/bin/p-link -> ../lib/debian-med/bin/plink lrwxrwxrwx root/root 0 2017-12-08 10:15 ./usr/bin/plink1 -> ../lib/debian-med/bin/plink drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 3182800 2017-12-08 10:15 ./usr/lib/debian-med/bin/plink drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/share/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/share/man/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/share/man/man1/ lrwxrwxrwx root/root 0 2017-12-08 10:15 ./usr/lib/debian-med/share/man/man1/plink.1.gz -> ../../../../../share/man/man1/p-link.1.gz drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/lib/plink/ lrwxrwxrwx root/root 0 2017-12-08 10:15 ./usr/lib/plink/plink -> ../debian-med/bin/plink drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/doc/plink/ -rw-r--r-- root/root 566 2017-12-08 10:15 ./usr/share/doc/plink/NEWS.Debian.gz -rw-r--r-- root/root 1894 2017-12-08 10:15 ./usr/share/doc/plink/README.Debian -rw-r--r-- root/root 1287 2007-07-27 14:51 ./usr/share/doc/plink/README.txt -rw-r--r-- root/root 1644 2017-12-08 10:15 ./usr/share/doc/plink/changelog.Debian.gz -rw-r--r-- root/root 2290 2017-12-08 10:15 ./usr/share/doc/plink/copyright drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/doc/plink/examples/ -rw-r--r-- root/root 358 2017-12-08 10:15 ./usr/share/doc/plink/examples/README -rw-r--r-- root/root 267 2017-12-08 10:15 ./usr/share/doc/plink/examples/expected.plink.assoc -rw-r--r-- root/root 126 2017-12-08 10:15 ./usr/share/doc/plink/examples/expected.plink.frq -rw-r--r-- root/root 23 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.map -rw-r--r-- root/root 138 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.ped drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/man/ drwxr-xr-x root/root 0 2017-12-08 10:15 ./usr/share/man/man1/ -rw-r--r-- root/root 688 2017-12-08 10:15 ./usr/share/man/man1/p-link.1.gz lrwxrwxrwx root/root 0 2017-12-08 10:15 ./usr/share/man/man1/plink1.1.gz -> p-link.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 306316 Build-Time: 485 Distribution: bionic-proposed Host Architecture: amd64 Install-Time: 13 Job: plink_1.07+dfsg-1.dsc Machine Architecture: amd64 Package: plink Package-Time: 500 Source-Version: 1.07+dfsg-1 Space: 306316 Status: successful Version: 1.07+dfsg-1 -------------------------------------------------------------------------------- Finished at 20171208-1716 Build needed 00:08:20, 306316k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 Scanning for processes to kill in build PACKAGEBUILD-13832550 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 Stopping target for build PACKAGEBUILD-13832550 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=amd64 PACKAGEBUILD-13832550 Removing build PACKAGEBUILD-13832550