RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-040 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 17:07:18 ntpdate[1810]: adjust time server 10.211.37.1 offset 0.005736 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 /home/buildd/filecache-default/b6762bcd0bec7d108ffb0fb3fb0b7d1ce32df8bb Creating target for build PACKAGEBUILD-13832553 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 Starting target for build PACKAGEBUILD-13832553 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 '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-13832553 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 Updating target for build PACKAGEBUILD-13832553 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 i386 Packages [1006 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe i386 Packages [8304 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4897 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 Packages [59.9 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [28.4 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe i386 Packages [177 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [98.1 kB] Fetched 15.5 MB in 7s (2164 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-i686-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 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 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 101 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 62.6 MB of archives. After this operation, 1056 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main i386 base-files i386 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main i386 bsdutils i386 1:2.30.2-0.1ubuntu1 [62.5 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main i386 coreutils i386 8.26-3ubuntu4 [1283 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 debianutils i386 4.8.3 [86.3 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 dpkg i386 1.19.0.4ubuntu1 [1166 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main i386 libc6-dev i386 2.26-0ubuntu2 [2144 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main i386 libc-dev-bin i386 2.26-0ubuntu2 [67.0 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 linux-libc-dev i386 4.14.0-11.13 [960 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main i386 libquadmath0 i386 7.2.0-17ubuntu1 [205 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main i386 libitm1 i386 7.2.0-17ubuntu1 [30.3 kB] Get:11 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http://ftpmaster.internal/ubuntu bionic/main i386 g++-7 i386 7.2.0-17ubuntu1 [7800 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main i386 gcc-7 i386 7.2.0-17ubuntu1 [7664 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main i386 libgcc-7-dev i386 7.2.0-17ubuntu1 [2399 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main i386 libstdc++-7-dev i386 7.2.0-17ubuntu1 [1498 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main i386 libstdc++6 i386 7.2.0-17ubuntu1 [429 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libgmp10 i386 2:6.1.2+dfsg-1.1 [246 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main i386 libbinutils i386 2.29.1-10ubuntu1 [551 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main i386 binutils i386 2.29.1-10ubuntu1 [3412 B] Get:29 http://ftpmaster.internal/ubuntu bionic/main i386 binutils-common i386 2.29.1-10ubuntu1 [190 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main i386 binutils-i686-linux-gnu i386 2.29.1-10ubuntu1 [1998 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libsmartcols1 i386 2.30.2-0.1ubuntu1 [85.6 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main i386 libfdisk1 i386 2.30.2-0.1ubuntu1 [173 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main i386 libpcre3 i386 2:8.39-8 [228 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main i386 libselinux1 i386 2.7-2 [73.0 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main i386 libmount1 i386 2.30.2-0.1ubuntu1 [143 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main i386 fdisk i386 2.30.2-0.1ubuntu1 [115 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main i386 util-linux i386 2.30.2-0.1ubuntu1 [905 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main i386 base-passwd i386 3.5.44 [47.8 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main i386 libc-bin i386 2.26-0ubuntu2 [569 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main i386 sysvinit-utils i386 2.88dsf-59.10ubuntu1 [19.3 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main i386 libudev1 i386 235-3ubuntu2 [58.2 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main i386 libapt-pkg5.0 i386 1.6~alpha5 [847 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main i386 debconf all 1.5.65 [124 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 adduser all 3.116ubuntu1 [163 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main i386 libgpg-error0 i386 1.27-5 [40.2 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main i386 libgcrypt20 i386 1.8.1-4 [398 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main i386 gpgv i386 2.1.15-1ubuntu8 [206 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main i386 libseccomp2 i386 2.3.1-2.1ubuntu3 [35.4 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main i386 apt i386 1.6~alpha5 [1169 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main i386 libapparmor1 i386 2.11.0-2ubuntu18 [30.3 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main i386 libcap2 i386 1:2.25-1.2 [13.4 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main i386 libip4tc0 i386 1.6.1-2ubuntu2 [20.4 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main i386 mount i386 2.30.2-0.1ubuntu1 [115 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main i386 systemd i386 235-3ubuntu2 [2926 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main i386 libsystemd0 i386 235-3ubuntu2 [213 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main i386 systemd-sysv i386 235-3ubuntu2 [13.1 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main i386 libcap-ng0 i386 0.7.7-3.1 [11.2 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main i386 libcomerr2 i386 1.43.7-1 [11.7 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main i386 libsemanage-common all 2.7-2 [6916 B] Get:70 http://ftpmaster.internal/ubuntu bionic/main i386 libsemanage1 i386 2.7-2 [93.4 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main i386 libss2 i386 1.43.7-1 [11.6 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main i386 libnettle6 i386 3.3-2 [109 kB] Get:73 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libsqlite3-0 i386 3.21.0-1 [526 kB] Get:84 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libssl1.0.0 i386 1.0.2g-1ubuntu15 [907 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main i386 multiarch-support i386 2.26-0ubuntu2 [6830 B] Get:86 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 openssl i386 1.0.2g-1ubuntu15 [507 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main i386 tzdata all 2017c-1 [188 kB] Get:88 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libgssapi-krb5-2 i386 1.15.2-2 [130 kB] Get:89 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libkrb5-3 i386 1.15.2-2 [301 kB] Get:90 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libkrb5support0 i386 1.15.2-2 [33.1 kB] Get:91 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libk5crypto3 i386 1.15.2-2 [89.5 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main i386 libkeyutils1 i386 1.5.9-9.2ubuntu1 [9544 B] Get:93 http://ftpmaster.internal/ubuntu bionic/main i386 libidn2-0 i386 2.0.4-1 [94.8 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main i386 libpng16-16 i386 1.6.34-1 [183 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/universe i386 apt-transport-https all 1.6~alpha5 [1692 B] Get:96 http://ftpmaster.internal/ubuntu bionic/main i386 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main i386 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main i386 build-essential i386 12.4ubuntu1 [4752 B] Get:99 http://ftpmaster.internal/ubuntu bionic/main i386 libpsl5 i386 0.19.1-4 [41.9 kB] Get:100 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libcurl3-gnutls i386 7.55.1-1ubuntu3 [214 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main i386 optipng i386 0.7.6-1ubuntu1 [87.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.6 MB in 2s (26.0 MB/s) (Reading database ... 12671 files and directories 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Preparing to unpack .../base-files_10ubuntu1_i386.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 ... 12671 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.2-0.1ubuntu1_i386.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 ... 12671 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_i386.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12671 files and directories currently installed.) 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Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up build-essential (12.4ubuntu1) ... Setting up libcurl3-gnutls:i386 (7.55.1-1ubuntu3) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13832553 i386 bionic-proposed -c chroot:build-PACKAGEBUILD-13832553 --arch=i386 --dist=bionic-proposed --nolog plink_1.07+dfsg-1.dsc Initiating build PACKAGEBUILD-13832553 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 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-040.buildd +==============================================================================+ | plink 1.07+dfsg-1 (i386) 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: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/plink-YFVh73/plink-1.07+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/plink-YFVh73' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13832553/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-8MhI0Z/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-8MhI0Z/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8MhI0Z/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8MhI0Z/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8MhI0Z/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-8MhI0Z/apt_archive ./ Packages [523 B] Fetched 2856 B in 0s (51.1 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-8MhI0Z/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 (33.3 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12674 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.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-1VAy9g/apt_archive/sbuild-build-depends-plink-dummy.deb'. Ign:1 copy:/<>/resolver-1VAy9g/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1VAy9g/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-1VAy9g/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1VAy9g/apt_archive ./ Sources [215 B] Get:5 copy:/<>/resolver-1VAy9g/apt_archive ./ Packages [534 B] Fetched 2868 B in 0s (102 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 17.1 MB of archives. After this operation, 63.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-1VAy9g/apt_archive ./ sbuild-build-depends-plink-dummy 0.invalid.0 [860 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main i386 groff-base i386 1.22.3-9 [1163 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main i386 libbsd0 i386 0.8.6-3 [44.9 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 bsdmainutils i386 9.0.14ubuntu1 [181 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 libpipeline1 i386 1.5.0-1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main i386 man-db i386 2.7.6.1-4 [907 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main i386 libmagic-mgc i386 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main i386 libmagic1 i386 1:5.32-1 [75.0 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main i386 file i386 1:5.32-1 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main i386 libglib2.0-0 i386 2.54.1-1ubuntu1 [1231 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main i386 libicu60 i386 60.1-1ubuntu2 [8185 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libxml2 i386 2.9.4+dfsg1-5.1ubuntu1 [703 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main i386 gettext-base i386 0.19.8.1-4ubuntu1 [50.7 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main i386 libsigsegv2 i386 2.11-1 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main i386 m4 i386 1.4.18-1 [196 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main i386 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main i386 autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main i386 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main i386 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main i386 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main i386 dh-autoreconf all 15 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main i386 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main i386 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main i386 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main i386 libcroco3 i386 0.6.12-1 [87.5 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main i386 gettext i386 0.19.8.1-4ubuntu1 [1097 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main i386 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main i386 debhelper all 10.10.9ubuntu1 [871 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.1 MB in 0s (22.7 MB/s) (Reading database ... 12674 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_i386.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../01-libbsd0_0.8.6-3_i386.deb ... Unpacking libbsd0:i386 (0.8.6-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.14ubuntu1_i386.deb ... Unpacking bsdmainutils (9.0.14ubuntu1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.0-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-4_i386.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_i386.deb ... 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Unpacking gettext-base (0.19.8.1-4ubuntu1) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../12-libsigsegv2_2.11-1_i386.deb ... Unpacking libsigsegv2:i386 (2.11-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-1_i386.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20161112.1+nmu1_all.deb ... Unpacking autotools-dev (20161112.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15.1-3ubuntu1_all.deb ... Unpacking automake (1:1.15.1-3ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-4ubuntu1_all.deb ... Unpacking autopoint (0.19.8.1-4ubuntu1) ... 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Unpacking dh-strip-nondeterminism (0.040-1) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../24-libcroco3_0.6.12-1_i386.deb ... Unpacking libcroco3:i386 (0.6.12-1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-4ubuntu1_i386.deb ... Unpacking gettext (0.19.8.1-4ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.10.9ubuntu1_all.deb ... Unpacking debhelper (10.10.9ubuntu1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../29-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu2_i386.deb ... Unpacking zlib1g-dev:i386 (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_i386.deb ... Unpacking sbuild-build-depends-plink-dummy (0.invalid.0) ... Setting up libicu60:i386 (60.1-1ubuntu2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:i386 (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:i386 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:i386 (0.8.6-3) ... Setting up libxml2:i386 (2.9.4+dfsg1-5.1ubuntu1) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:i386 (1:5.32-1) ... Setting up libcroco3:i386 (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:i386 (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 ... 14508 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 (i686) 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-i686-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 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 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-13832553 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13832553 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13832553 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 i386 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-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a 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:1109:61: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized] pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); ~~~~~^~~~~~~~~~ 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 -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a 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 -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a 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 " 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. dpkg-deb: building package 'plink-dbgsym' in 'debian/.debhelper/scratch-space/build-plink/plink-dbgsym_1.07+dfsg-1_i386.deb'. 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: Truncating usr/share/doc/plink/changelog.Debian.gz to topmost ten records 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_i386.deb'. Renaming plink-dbgsym_1.07+dfsg-1_i386.deb to plink-dbgsym_1.07+dfsg-1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../plink_1.07+dfsg-1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build plink-1.07+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171208-1720 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ plink_1.07+dfsg-1_i386.changes: ------------------------------- Format: 1.8 Date: Fri, 08 Dec 2017 11:15:55 +0100 Source: plink Binary: plink Architecture: i386 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: cc914c75b27fba3db1a9ef5a79efb69ee8873ca9 18688204 plink-dbgsym_1.07+dfsg-1_i386.ddeb 0b29af150d76a71b277f904369db173ede072345 4949 plink_1.07+dfsg-1_i386.buildinfo ad2cbb21e6b3f3df70ff7ee23435ef6fbe5b126e 1171488 plink_1.07+dfsg-1_i386.deb Checksums-Sha256: 5e670d5ecd86095a4a641bba30fab02625b594c4e0d9f08eee8706d93ff1ce78 18688204 plink-dbgsym_1.07+dfsg-1_i386.ddeb 89f96022c77e08ef3387ef40afbb9da2125706ef8556abf42376fc9236081b82 4949 plink_1.07+dfsg-1_i386.buildinfo 5368943c0d1130d77273782078889b22b213e7ad5a5cad4ef9ef80f4b88e9e06 1171488 plink_1.07+dfsg-1_i386.deb Files: 3ddce95ebaaf1747ade9b2675112dd40 18688204 debug optional plink-dbgsym_1.07+dfsg-1_i386.ddeb 91fbd2b77614e135b62955b2e1048bdf 4949 science optional plink_1.07+dfsg-1_i386.buildinfo 5ed131865d31df0baa6d8a0814cdda3f 1171488 science optional plink_1.07+dfsg-1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ plink_1.07+dfsg-1_i386.deb -------------------------- new debian package, version 2.0. size 1171488 bytes: control archive=1308 bytes. 1142 bytes, 27 lines control 848 bytes, 12 lines md5sums Package: plink Version: 1.07+dfsg-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3492 Depends: libc6 (>= 2.4), 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 3526328 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: i386 Build-Space: 226752 Build-Time: 687 Distribution: bionic-proposed Host Architecture: i386 Install-Time: 17 Job: plink_1.07+dfsg-1.dsc Machine Architecture: amd64 Package: plink Package-Time: 706 Source-Version: 1.07+dfsg-1 Space: 226752 Status: successful Version: 1.07+dfsg-1 -------------------------------------------------------------------------------- Finished at 20171208-1720 Build needed 00:11:46, 226752k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 Scanning for processes to kill in build PACKAGEBUILD-13832553 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 Stopping target for build PACKAGEBUILD-13832553 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-13832553 Removing build PACKAGEBUILD-13832553