sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build00.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ plink 1.07-3 (armhf) 04 May 2012 00:10 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: plink Version: 1.07-3 Source Version: 1.07-3 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/plink-6gVndK/plink-1.07' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/plink-6gVndK' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-950b084a-f0ca-4790-bb34-0dfb8c0b35ce' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'plink' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/plink/trunk/ Need to get 586 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main plink 1.07-3 (dsc) [1359 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main plink 1.07-3 (tar) [577 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main plink 1.07-3 (diff) [7367 B] Fetched 586 kB in 0s (6263 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-RePE2C/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10678 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), zlib1g-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), zlib1g-dev dpkg-deb: building package `sbuild-build-depends-plink-dummy' in `/«BUILDDIR»/resolver-QLvykq/apt_archive/sbuild-build-depends-plink-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install plink build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-plink-dummy zlib1g-dev debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/9557 kB of archives. After this operation, 24.6 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.0-4_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ... Selecting previously unselected package zlib1g-dev:armhf. Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-plink-dummy. Unpacking sbuild-build-depends-plink-dummy (from .../sbuild-build-depends-plink-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up zlib1g-dev:armhf (1:1.2.6.dfsg-2) ... Setting up sbuild-build-depends-plink-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.12-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-plink-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon Apr 23 08:26:19 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./plink_1.07-3.dsc dpkg-source: info: extracting plink in plink-1.07 dpkg-source: info: unpacking plink_1.07.orig.tar.gz dpkg-source: info: unpacking plink_1.07-3.debian.tar.gz dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-950b084a-f0ca-4790-bb34-0dfb8c0b35ce SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package plink dpkg-buildpackage: source version 1.07-3 dpkg-source --before-build plink-1.07 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_clean make[2]: Entering directory `/«PKGBUILDDIR»' rm -f *.o *~ make[2]: Leaving directory `/«PKGBUILDDIR»' rm -f plink make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make CXXFLAGS='-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX' FORCE_DYNAMIC=1 make[2]: Entering directory `/«PKGBUILDDIR»' g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c plink.cpp In file included from plink.cpp:28:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from plink.cpp:35:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from plink.cpp:40:0: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp: In function 'int main(int, char**)': plink.cpp:764:13: warning: suggest parentheses around '&&' within '||' [-Wparentheses] plink.cpp:2106:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp: In member function 'void Plink::cleanUp()': plink.cpp:2359:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp:2362:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] plink.cpp:2366:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c options.cpp In file included from options.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c input.cpp In file included from input.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readData()': input.cpp:516:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:521:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:545:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:579:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:595:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:611:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:631:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readSet()': input.cpp:695:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:817:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:821:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readPhenoFile()': input.cpp:897:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:927:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:961:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:965:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1037:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1043:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1064:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::makePhenotype()': input.cpp:1208:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readCovariateFile()': input.cpp:1232:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1256:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1261:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readCovListFile()': input.cpp:1335:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1374:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1519:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1538:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'bool Plink::readMultiplePhenoFile()': input.cpp:1572:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1599:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1602:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1745:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:1764:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readSegmentFile(std::ifstream&)': input.cpp:1792:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': input.cpp:2116:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2172:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2200:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2210:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2215:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2225:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readFamFile(std::string)': input.cpp:2389:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2397:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2419:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp:2453:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': input.cpp:2471:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] input.cpp: In member function 'void Plink::updateAlleles()': input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] input.cpp: In member function 'void Plink::readData()': input.cpp:343:44: warning: 'PED' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c binput.cpp In file included from binput.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:157:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:176:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:186:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:261:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:339:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:351:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] binput.cpp:398:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c tinput.cpp In file included from tinput.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:218:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:246:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:256:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:261:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:271:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:309:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:591:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tinput.cpp:603:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c genome.cpp In file included from genome.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string displayLine(std::vector >&)': helper.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(matrix_t&)': helper.cpp:76:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:79:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(vector_t&)': helper.cpp:90:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'std::vector > CArgs::value(std::string, int)': helper.cpp:277:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector > parse2str(std::string)': helper.cpp:306:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:307:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:309:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector parse2int(std::string)': helper.cpp:323:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': helper.cpp:461:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void summaryBasics(Plink&)': helper.cpp:595:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:611:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'double genotypingRate(Plink&, int)': helper.cpp:659:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:664:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:729:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void removeMissingPhenotypes(Plink&)': helper.cpp:775:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void geno2matrix(std::vector&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::string chromosomeName(int)': helper.cpp:952:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': helper.cpp:959:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'int getMarkerNumber(Plink&, std::string)': helper.cpp:966:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'bool seeChromosome(Plink&, int)': helper.cpp:973:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector getChromosomeRange(Plink&)': helper.cpp:1040:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void checkFileExists(std::vector >)': helper.cpp:1172:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::prettyPrintLengths()': helper.cpp:1264:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1267:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1273:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:1391:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2462:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2491:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnCase()': helper.cpp:2510:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnControl()': helper.cpp:2530:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnMale()': helper.cpp:2549:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnFemale()': helper.cpp:2568:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnFounder()': helper.cpp:2587:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::filterOnNonFounder()': helper.cpp:2606:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::attribFilterSNP()': helper.cpp:2638:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2671:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In member function 'void Plink::attribFilterInd()': helper.cpp:2722:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp:2756:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void makePersonMap(Plink&, std::map, Individual*>&)': helper.cpp:2935:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'void smoother(Plink&, vector_t&, int, vector_t&, vector_t&, std::vector&)': helper.cpp:2959:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] helper.cpp: In function 'double getDouble(std::string, std::string)': helper.cpp:407:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': helper.cpp:393:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In function 'int getInt(std::string, std::string)': helper.cpp:380:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'double CArgs::value_double(std::string)': helper.cpp:256:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': helper.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'int CArgs::value_int(std::string)': helper.cpp:232:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:219:1: warning: control reaches end of non-void function [-Wreturn-type] helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c stats.cpp In file included from helper.h:24:0, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1483:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1515:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp:1521:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c filters.cpp In file included from filters.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:123:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:132:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:155:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:163:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:198:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:273:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] filters.cpp:591:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:611:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:739:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:762:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1078:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1091:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1143:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1165:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] filters.cpp: In member function 'void Plink::thinSNPs()': filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c locus.cpp In file included from locus.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c multi.cpp In file included from multi.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:304:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:357:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:372:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c crandom.cpp g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c cluster.cpp In file included from helper.h:24:0, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:452:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:511:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:492:8: warning: unused variable 'size' [-Wunused-variable] cluster.cpp:626:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:648:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:651:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:784:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:786:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:919:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:954:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:955:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:975:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:976:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1038:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1041:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1049:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1050:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1060:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1061:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1107:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1110:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1133:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1163:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1169:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'double cldist(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1204:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'double groupAvgLink(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1228:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1229:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool homogeneous_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1254:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1255:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool spec_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1272:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1276:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In function 'bool pairable_cluster(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1290:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1291:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp: In member function 'void Plink::groupGenome()': cluster.cpp:1643:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1661:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cluster.cpp:1664:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c mds.cpp In file included from mds.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:191:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:279:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c output.cpp In file included from output.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:86:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:89:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::display_twolocus()': output.cpp:402:28: warning: variable 'loc1' set but not used [-Wunused-but-set-variable] output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:526:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:553:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::keep2SetsForGenome()': output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] output.cpp: In member function 'void Plink::outputSetFile()': output.cpp:2200:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2322:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::setTable()': output.cpp:2367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::writeSetFile()': output.cpp:2409:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp:2412:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] output.cpp: In member function 'void Plink::display_pairList()': output.cpp:145:65: warning: 'i2' may be used uninitialized in this function [-Wuninitialized] output.cpp:144:65: warning: 'i1' may be used uninitialized in this function [-Wuninitialized] output.cpp: In member function 'void Plink::display_indivReport()': output.cpp:69:36: warning: 'i1' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c informative.cpp In file included from informative.cpp:18:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp:102:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] informative.cpp:105:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from assoc.cpp:29:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': assoc.cpp:395:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:741:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:744:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:785:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp:788:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c epi.cpp In file included from epi.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:154:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:161:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] epi.cpp:438:12: warning: unused variable 'zero' [-Wunused-variable] epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c prephap.cpp In file included from prephap.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from prephap.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp: In member function 'void HaploPhase::readTagFile()': prephap.cpp:226:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:283:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:412:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:416:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:420:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:470:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp: In member function 'void HaploPhase::makeSlidingWindow(std::string)': prephap.cpp:533:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] prephap.cpp:560:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c phase.cpp In file included from phase.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from phase.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from phase.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': phase.cpp:373:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': phase.cpp:472:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::performAlternEM()': phase.cpp:678:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1187:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1238:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1280:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1299:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1575:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp:1843:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c trio.cpp In file included from trio.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:272:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:335:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:342:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:350:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:474:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:492:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:504:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:871:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:882:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:895:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:931:6: warning: unused variable 'tmp' [-Wunused-variable] trio.cpp:936:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:943:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:1048:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp: In member function 'void Plink::makeMissingParents()': trio.cpp:1236:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] trio.cpp:1245:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c tdt.cpp In file included from tdt.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] tdt.cpp:132:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:144:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:210:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:234:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:327:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:330:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:412:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:415:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:557:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:668:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:776:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tdt.cpp:937:58: warning: 'zt' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c genepi.cpp In file included from genepi.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] genepi.cpp: In function 'long double pillai(int, int, int, double)': genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:489:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:497:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:506:10: warning: unused variable 'n12' [-Wunused-variable] genepi.cpp:507:10: warning: unused variable 'ne' [-Wunused-variable] genepi.cpp: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': genepi.cpp:1025:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:1033:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genepi.cpp:1043:10: warning: unused variable 'n12' [-Wunused-variable] genepi.cpp:1044:10: warning: unused variable 'ne' [-Wunused-variable] genepi.cpp:1064:10: warning: unused variable 'nind' [-Wunused-variable] genepi.cpp: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:840:83: warning: 'cancor1_pos' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c sets.cpp In file included from sets.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from sets.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::sizeSets()': sets.cpp:37:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:52:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:59:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:62:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::pruneMC(Plink&, bool, double)': sets.cpp:129:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:176:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::dropNotSet(Plink&)': sets.cpp:216:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:218:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:236:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:237:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:323:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:329:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:332:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:370:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:413:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:619:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:631:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:632:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:642:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:643:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::profileTestScore()': sets.cpp:703:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:713:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': sets.cpp:905:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:975:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::fitStepwiseModel()': sets.cpp:1042:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c perm.cpp In file included from perm.h:17:0, from perm.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp:145:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'void Perm::setOriginalRanking(vector_t&)': perm.cpp:187:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp:199:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] perm.cpp: In member function 'bool Perm::update(std::vector&, std::vector&)': perm.cpp:273:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c mh.cpp In file included from perm.h:17:0, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genedrop.cpp: In member function 'void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c gxe.cpp In file included from helper.h:24:0, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c merge.cpp In file included from merge.cpp:22:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:377:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:395:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:403:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:426:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:722:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:733:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:784:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:830:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp:842:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c hotel.cpp In file included from hotel.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] hotel.cpp:173:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c multiple.cpp In file included from helper.h:24:0, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] multiple.cpp:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c haploCC.cpp In file included from haploCC.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploCC.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp: In member function 'void HaploPhase::haplotypicCC(std::map&, int, bool)': haploCC.cpp:48:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:62:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:79:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:93:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:357:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] haploCC.cpp:375:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploCC.cpp:392:39: warning: suggest parentheses around '&&' within '||' [-Wparentheses] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c haploTDT.cpp In file included from haploTDT.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploTDT.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c poo.cpp In file included from poo.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:195:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:198:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:328:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:130:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:146:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:180:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] webcheck.cpp:218:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:89:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:97:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:315:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:648:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:657:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linear.cpp: In member function 'double LinearModel::getPValue()': linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:100:18: warning: 'irow' may be used uninitialized in this function [-Wuninitialized] linear.cpp:101:18: warning: 'icol' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c bmerge.cpp In file included from bmerge.cpp:22:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] bmerge.cpp:357:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:390:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:409:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:417:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:440:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:549:11: warning: variable 'indn' set but not used [-Wunused-but-set-variable] bmerge.cpp:697:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] bmerge.cpp:839:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:871:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bmerge.cpp:883:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c parse.cpp In file included from parse.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c mishap.cpp In file included from mishap.cpp:17:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from mishap.cpp:20:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp: In member function 'void Plink::performMisHapTests()': mishap.cpp:209:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:236:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:349:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] mishap.cpp:373:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c legacy.cpp In file included from helper.h:24:0, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:377:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:381:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:384:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:390:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:395:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:415:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:424:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:460:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:461:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:462:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:467:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp:480:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': legacy.cpp:203:27: warning: 'last' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c homozyg.cpp In file included from helper.h:24:0, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:695:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:722:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:756:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:773:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:861:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1178:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1331:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1437:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1441:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp:1461:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:24: warning: value computed is not used [-Wunused-value] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c segment.cpp In file included from helper.h:24:0, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:14: warning: variable 'p' set but not used [-Wunused-but-set-variable] segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2380:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2382:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2412:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2414:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2416:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2443:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2445:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2447:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2474:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2476:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] segment.cpp:2478:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c model.cpp In file included from model.cpp:15:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from model.cpp:17:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'void Model::setMissing(std::vector&)': model.cpp:132:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp:367:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp:374:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:850:1: warning: control reaches end of non-void function [-Wreturn-type] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c logistic.cpp In file included from helper.h:24:0, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] logistic.cpp: In member function 'double LogisticModel::getPValue()': logistic.cpp:327:8: warning: unused variable 'okay' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c glm.cpp In file included from helper.h:24:0, from glm.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from glm.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': glm.cpp:294:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:344:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:355:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:423:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] glm.cpp:610:37: warning: 'df' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c dcdflib.cpp dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:55: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp:6088:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6112:52: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6153:52: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] dcdflib.cpp: In function 'double dt1(double*, double*, double*)': dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp:6831:1: warning: missing braces around initializer for 'double [5]' [-Wmissing-braces] dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:64: warning: suggest parentheses around '&&' within '||' [-Wparentheses] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c elf.cpp In file included from helper.h:24:0, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp:939:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:400:48: warning: 'wt' may be used uninitialized in this function [-Wuninitialized] elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1142:19: warning: 'p_gcnt' may be used uninitialized in this function [-Wuninitialized] elf.cpp:1165:15: warning: 'p_cnt' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c dfam.cpp In file included from dfam.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:86:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:96:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:106:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:157:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:240:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dfam.cpp:271:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:378:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] dfam.cpp:504:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c fisher.cpp In file included from helper.h:24:0, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:267:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:273:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:450:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:501:59: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:509:54: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:563:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:751:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:1555:52: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp:1597:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c linput.cpp In file included from linput.cpp:25:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:136:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:146:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:164:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:200:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] linput.cpp:209:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c sockets.cpp In file included from helper.h:24:0, from sockets.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c lookup.cpp In file included from helper.h:24:0, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp:203:8: warning: unused variable 'totalSNPs' [-Wunused-variable] lookup.cpp:204:8: warning: unused variable 'gcount' [-Wunused-variable] lookup.cpp:272:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c proxy.cpp In file included from proxy.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from proxy.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:314:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:332:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:854:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1332:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1401:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] proxy.cpp:939:58: warning: 'ref' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c pdriver.cpp In file included from pdriver.cpp:16:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from pdriver.cpp:18:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] pdriver.cpp: In member function 'void Plink::proxyWrapper()': pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c haploQTL.cpp In file included from haploQTL.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haploQTL.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploQTL.cpp: In member function 'void HaploPhase::haplotypicQTL(std::map&, int, bool)': haploQTL.cpp:83:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haploQTL.cpp:145:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c haplohelper.cpp In file included from haplohelper.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplohelper.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplohelper.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::imputeAllHaplotypes()': haplohelper.cpp:104:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:134:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::setTestHaplotype(std::string)': haplohelper.cpp:337:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::reportPhase()': haplohelper.cpp:396:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:413:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::reportPhaseWideFormat()': haplohelper.cpp:487:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::imputeHaplotypes(int, bool&, bool&)': haplohelper.cpp:754:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:802:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::rsq_internal(boolvec_t&, boolvec_t&, boolvec_t&, boolvec_t&)': haplohelper.cpp:850:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:850:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:850:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:851:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:957:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1251:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1252:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp:1477:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c haplowindow.cpp In file included from haplowindow.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplowindow.cpp:27:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from haplowindow.cpp:28:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::prunePhase(int, double)': haplowindow.cpp:558:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:574:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:691:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:751:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:791:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:798:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:868:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:872:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp: In member function 'void HaploWindow::reportPhase()': haplowindow.cpp:949:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] haplowindow.cpp:966:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c genogroup.cpp In file included from genogroup.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genogroup.cpp:24:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genogroup.cpp:28:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c nonfounderphasing.cpp In file included from nonfounderphasing.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from nonfounderphasing.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from nonfounderphasing.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nonfounderphasing.cpp: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': nonfounderphasing.cpp:668:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c clumpld.cpp In file included from helper.h:24:0, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from clumpld.cpp:21:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp: In member function 'std::vector clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:137:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:173:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:201:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:204:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:480:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:520:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:611:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] clumpld.cpp:1097:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c genoerr.cpp In file included from genoerr.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genoerr.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from genoerr.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': genoerr.cpp:157:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:189:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:190:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:225:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:315:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:328:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:347:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genoerr.cpp:358:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c em.cpp In file included from em.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from em.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from em.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp: In member function 'void HaploPhase::performEM_original()': em.cpp:89:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:97:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:106:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:128:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:132:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:162:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] em.cpp:166:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c impute.cpp In file included from impute.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from impute.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from impute.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp: In constructor 'probabilisticGenotype::probabilisticGenotype()': impute.cpp:40:25: warning: suggest parentheses around assignment used as truth value [-Wparentheses] impute.cpp: In member function 'void HaploPhase::updateForImputation()': impute.cpp:105:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:144:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:161:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] impute.cpp:313:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c metaem.cpp In file included from metaem.cpp:24:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from metaem.cpp:27:0: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from metaem.cpp:28:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaem.cpp: In member function 'void HaploPhase::enumeratePhasedWindows(int)': metaem.cpp:239:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c profile.cpp In file included from profile.cpp:23:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] profile.cpp:390:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp:402:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp:421:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] profile.cpp:629:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] profile.cpp: In function 'void scoreRanges(int, std::vector&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c nlist.cpp In file included from helper.h:24:0, from nlist.h:21, from nlist.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector NList::expandNumberList(std::vector&)': nlist.cpp:107:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:124:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:151:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:160:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp: In member function 'std::vector > NList::tokenize(std::string)': nlist.cpp:189:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:239:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] nlist.cpp:253:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from whap.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)': whap.cpp:334:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:393:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:454:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:456:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:508:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:511:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:619:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:670:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:793:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:793:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:986:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1015:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1048:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1118:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1129:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1142:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1162:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1197:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1231:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1290:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1326:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1334:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In member function 'void Chap::setSNPList(std::vector&, ChapModel&)': whap.cpp:1389:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp: In function 'void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)': whap.cpp:1425:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] whap.cpp:1434:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c simul.cpp In file included from helper.h:24:0, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:679:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp: In member function 'void Plink::simulateSNPs_QT()': simul.cpp:1146:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:1211:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] simul.cpp:1358:23: warning: unused variable 'cumU' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:192:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:247:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:298:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:381:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:395:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:403:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:471:11: warning: unused variable 'ip' [-Wunused-variable] gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] gvar.cpp:549:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:553:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] gvar.cpp:556:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -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:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] cnv.cpp:678:36: warning: variable 'is' set but not used [-Wunused-but-set-variable] cnv.cpp:815:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp:825:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp:1031:25: warning: variable 'i2' set but not used [-Wunused-but-set-variable] cnv.cpp:1103:36: warning: variable 'il' set but not used [-Wunused-but-set-variable] cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:20: warning: statement has no effect [-Wunused-value] cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c step.cpp In file included from helper.h:24:0, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c greport.cpp In file included from greport.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:147:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:156:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:169:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:240:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c flip.cpp In file included from helper.h:24:0, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c qualscores.cpp In file included from helper.h:24:0, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c cnvqt.cpp In file included from helper.h:24:0, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c cfamily.cpp In file included from cfamily.cpp:18:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:221:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:237:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:276:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cfamily.cpp:288:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c setscreen.cpp In file included from setscreen.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:110:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:188:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] setscreen.cpp:196:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c idhelp.cpp In file included from idhelp.cpp:18:0: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from idhelp.cpp:19:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:63:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'bool IDHelper::matchIndividual(IDGroup*, std::map >&)': idhelp.cpp:136:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:169:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:221:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:296:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:510:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:542:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:547:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:553:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] idhelp.cpp:584:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:594:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:678:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:727:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:742:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:745:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:747:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:757:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] idhelp.cpp:772:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:790:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:794:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:808:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:836:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:888:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:894:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:903:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:922:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:950:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:975:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1000:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1003:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1013:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] idhelp.cpp:1025:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1028:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] idhelp.cpp:1070:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1085:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1110:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1128:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1183:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1189:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1236:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1242:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] idhelp.cpp:1346:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1424:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1440:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1631:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1648:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1649:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1654:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1675:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1684:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1692:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1710:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1733:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1735:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1770:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1784:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1801:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1903:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1937:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1957:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1964:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1986:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2018:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2024:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2030:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2034:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2070:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] idhelp.cpp:2167:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2168:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2201:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] idhelp.cpp:2234:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c tag.cpp In file included from helper.h:24:0, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c hapglm.cpp In file included from helper.h:24:0, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from hapglm.cpp:25:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c lookup2.cpp In file included from helper.h:24:0, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:203:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:280:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] lookup2.cpp:325:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c blox.cpp In file included from blox.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from blox.cpp:23:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp: In member function 'std::map > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] blox.cpp:418:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp:427:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] blox.cpp:123:16: warning: unused variable 'fourGameteCutoff' [-Wunused-variable] blox.cpp: In member function 'void PairwiseLinkage::calculateCI()': blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] blox.cpp:570:3: warning: 'pB2' may be used uninitialized in this function [-Wuninitialized] blox.cpp:505:21: warning: 'pB1' may be used uninitialized in this function [-Wuninitialized] blox.cpp:503:21: warning: 'pA2' may be used uninitialized in this function [-Wuninitialized] blox.cpp:503:21: warning: 'pA1' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c zed.cpp In file included from helper.h:24:0, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c dosage.cpp In file included from dosage.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from dosage.cpp:23:0: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp: In member function 'void Plink::processDosageFile()': dosage.cpp:110:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:513:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:548:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:581:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:601:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:695:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:750:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:989:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:1170:11: warning: unused variable 'statistic' [-Wunused-variable] dosage.cpp:1252:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:1310:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] dosage.cpp:1179:31: warning: 'snp_code' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c annot.cpp In file included from annot.cpp:20:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:250:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:251:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:260:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:275:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] annot.cpp:300:9: warning: unused variable 'include' [-Wunused-variable] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c metaanal.cpp In file included from metaanal.cpp:21:0: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] metaanal.cpp:61:3: warning: when initialized here [-Wreorder] metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:182:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:203:23: warning: statement has no effect [-Wunused-value] metaanal.cpp:213:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:235:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:261:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:300:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] metaanal.cpp:482:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:637:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] metaanal.cpp:680:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c r.cpp In file included from Rconnection.h:42:0, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] In file included from helper.h:24:0, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from r.cpp:29:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wuninitialized] r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wuninitialized] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c Rconnection.cpp In file included from Rconnection.h:42:0, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] In file included from Rconnection.cpp:30:0: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.h:249:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -c zfstream.cpp g++ -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -DWITH_R_PLUGINS -DUNIX -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory `/«PKGBUILDDIR»' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/plink/usr/lib/plink/plink contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/plink/usr/lib/plink/plink was not linked against libdl.so.2 (it uses none of the library's symbols). dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `plink' in `../plink_1.07-3_armhf.deb'. dpkg-genchanges -B -mbuildd >../plink_1.07-3_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build plink-1.07 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120504-0105 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ plink_1.07-3_armhf.changes: ─────────────────────────── Format: 1.8 Date: Mon, 23 Apr 2012 07:23:07 +0000 Source: plink Binary: plink Architecture: armhf Version: 1.07-3 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: plink - whole-genome association analysis toolset Closes: 667325 Changes: plink (1.07-3) unstable; urgency=low . * debian/patches/gcc-4.7.patch: previous patch was incomplete because the same problem occured in more files. Now really Closes: #667325 Checksums-Sha1: c5f24fe1831949e64b8fec1165b540ce263ba6c5 1226888 plink_1.07-3_armhf.deb Checksums-Sha256: 03e620d5715e6de105f8c607edb241dbee73a7863a903d6e3d8d873e187a3457 1226888 plink_1.07-3_armhf.deb Files: bd752b3d9743d86af77b148fd6e36657 1226888 science optional plink_1.07-3_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ plink_1.07-3_armhf.deb ────────────────────── new debian package, version 2.0. size 1226888 bytes: control archive= 1058 bytes. 1045 bytes, 25 lines control 534 bytes, 8 lines md5sums Package: plink Version: 1.07-3 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2365 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Description: whole-genome association analysis toolset plink expects as input the data from SNP (single nucleotide polymorphism) chips of many individuals and their phenotypical description of a disease. It finds associations of single or pairs of DNA variations with a phenotype and can retrieve SNP annotation from an online source. . SNPs can evaluated individually or as pairs for their association with the disease phenotypes. The joint investigation of copy number variations is supported. A variety of statistical tests have been implemented. . Please note: The executable was renamed to p-link because of a name clash. Please read more about this in /usr/share/doc/README.Debian. drwxr-xr-x root/root 0 2012-05-04 01:04 ./ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/doc/plink/ -rw-r--r-- root/root 1406 2012-04-23 01:22 ./usr/share/doc/plink/changelog.Debian.gz drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/doc/plink/examples/ -rw-r--r-- root/root 138 2007-07-27 07:51 ./usr/share/doc/plink/examples/test.ped -rw-r--r-- root/root 23 2007-07-27 07:51 ./usr/share/doc/plink/examples/test.map -rw-r--r-- root/root 1287 2007-07-27 07:51 ./usr/share/doc/plink/README.txt -rw-r--r-- root/root 1590 2009-04-30 13:38 ./usr/share/doc/plink/README.Debian -rw-r--r-- root/root 2204 2012-04-22 23:56 ./usr/share/doc/plink/copyright drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/share/man/man1/ -rw-r--r-- root/root 672 2012-05-04 01:04 ./usr/share/man/man1/p-link.1.gz drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/lib/plink/ -rwxr-xr-x root/root 2364308 2012-05-04 01:04 ./usr/lib/plink/plink drwxr-xr-x root/root 0 2012-05-04 01:04 ./usr/bin/ lrwxrwxrwx root/root 0 2012-05-04 01:04 ./usr/bin/p-link -> ../lib/plink/plink ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* file* gettext* gettext-base* groff-base* html2text* intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* sbuild-build-depends-core-dummy* sbuild-build-depends-plink-dummy* zlib1g-dev* 0 upgraded, 0 newly installed, 21 to remove and 0 not upgraded. After this operation, 24.6 MB disk space will be freed. (Reading database ... 12089 files and directories currently installed.) Removing sbuild-build-depends-plink-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... Removing zlib1g-dev:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 135108 Build-Time: 3193 Distribution: testing Install-Time: 50 Job: plink_1.07-3 Package: plink Package-Time: 3260 Source-Version: 1.07-3 Space: 135108 Status: successful Version: 1.07-3 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120504-0105 Build needed 00:54:20, 135108k disc space