debian/0000755000000000000000000000000011745211013007161 5ustar debian/upstream0000644000000000000000000000075211745035327010764 0ustar Reference: Author: Shaun Purcell and Benjamin Neale and Kathe Todd-Brown and Lori Thomas and Manuel A. R. Ferreira and David Bender and Julian Maller and Pamela Sklar and Paul I. W. de Bakker and Mark J. Daly and Pak C. Sham Title: "PLINK: a toolset for whole-genome association and population-based linkage analysis" Journal: American Journal of Human Genetics Volume: 81 Number: 3 Pages: 559-75 Year: 2007 PMID: 17701901 URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950838/ debian/examples0000644000000000000000000000002211110210474010710 0ustar test.ped test.map debian/source/0000755000000000000000000000000011745035765010503 5ustar debian/source/format0000644000000000000000000000001411634154453011702 0ustar 3.0 (quilt) debian/p-link.10000644000000000000000000000214511176406064010451 0ustar .\" Hey, EMACS: -*- nroff -*- .TH P-LINK 1 "April 8, 2008" .SH NAME p-link \- whole genome SNP analysis .SH SYNOPSIS .B p-link --help .SH DESCRIPTION This binary was renamed from plink to p-link because there is a name clash between this plink and a part of the ssh clone putty. Please read /usr/share/doc/plink/README.Debian to learn more about this. P-link works on SNP datasets that have already been pre-analysed for their reliability and their calling to AA, BB or AB. It finds associations with a disease of single SNPs or pairs, determines haplotype blocks or retrieves information on SNPs from an online repository. This manual page must be insufficient. Please use the help option for a quick reminder of the options of p-link or turn to its home page with the online documentation or the downloadable manual. .SH SEE ALSO .BR http://pngu.mgh.harvard.edu/~purcell/plink .SH AUTHOR plink was written by Shaun Purcell .PP This manual page was written by Steffen Moeller , for the Debian project (but may be used by others). debian/README.source0000644000000000000000000000077011232075310011343 0ustar Upstream file deletion ---------------------- Mark of the ftpmasters has requested the gPLINK.jar to disappear. This removal will be automatically done if you are using the debian/get-orig-source script to obtain the upstream tarball. Upstream source patching ------------------------ This packages uses the program ‘quilt’ to apply patch from the ‘debian/patches’ directory. You can find instructions on how to use quilt in the following file: ‘/usr/share/doc/quilt/README.source’. debian/docs0000644000000000000000000000001311110210474010022 0ustar README.txt debian/copyright0000644000000000000000000000423411745176401011132 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: PLINK Upstream-Contact: Shaun Purcell Source: http://pngu.mgh.harvard.edu/~purcell/plink/dist/ Files: * Copyright: 2005-2009 Shaun Purcell License: GPL-2 Files: Rconnection.* Copyright: 2004 Simon Urbanek License: LGPL-2.1 Files: debian/* Copyright: 2008 Steffen Moeller 2009-2012 Andreas Tille License: GPL-2 License: GPL-2 This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License in version 2 of the license as published by the Free Software Foundation. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. License: LGPL-2.1 This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; version 2.1 of the License . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Leser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . Although this code is licensed under LGPL v2.1, we strongly encourage everyone modifying this software to contribute back any improvements and bugfixes to the project for the benefit all other users. Thank you. debian/compat0000644000000000000000000000000211745175236010377 0ustar 9 debian/get-orig-source0000644000000000000000000000221511745035677012143 0ustar #!/bin/sh # script to download and repack source package # Repackaging is needed because original archive is in zip format # and moreover gPLINK.jar has to be stripped from the tarball because # it is a binary without source BUILDTARBALLDEPENDS="unzip" missingdepends=`dpkg -l ${BUILDTARBALLDEPENDS} ${BUILDDEPS} | \ grep -v -e "^ii" -e "^|" -e "^++" -e "^ " -e "^..[^[:space:]]" | \ sed 's/^[a-z][a-z][[:space:]]\+\([^[:space:]]\+\)[[:space:]]\+.*/\1/'` if [ "$missingdepends" != "" ] ; then echo "Please install the following packages to rebuild the upstream source tarball:" echo $missingdepends exit -1 fi PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` VERSION=`uscan --verbose --force-download | \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"` mkdir -p ../tarballs cd ../tarballs UPSTREAMDIR="${PKG}-${VERSION}-src" unzip ../"$UPSTREAMDIR".zip rm -f "$UPSTREAMDIR"/gPLINK.jar GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$PKG"_"$VERSION".orig.tar.gz "$UPSTREAMDIR" rm -rf "$UPSTREAMDIR" debian/control0000644000000000000000000000243611745175232010605 0ustar Source: plink Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy Build-Depends: debhelper (>= 9), zlib1g-dev Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plink/trunk/ Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Package: plink Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} 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. debian/patches/0000755000000000000000000000000011745205065010622 5ustar debian/patches/gcc-4.7.patch0000644000000000000000000000413211745207021012677 0ustar Author: Rodolfo García Peñas , Dmitry Nezhevenko , Fernando Lemos Date: Sun, 22 Apr 2012 23:37:53 +0300 Bug-Closed: http://bugs.debian.org/667325 Description: Fix nested declaration which fails in gcc-4.7 For more detailed explanation see http://lists.debian.org/debian-mentors/2012/04/msg00410.html and the other mails in this thread --- plink-1.07.orig/sets.cpp +++ plink-1.07/sets.cpp @@ -768,11 +768,11 @@ ////////////////////////////////////////////// // Reset original missing status - vector::iterator i = PP->sample.begin(); - while ( i != PP->sample.end() ) + vector::iterator i_iter = PP->sample.begin(); + while ( i_iter != PP->sample.end() ) { - (*i)->missing = (*i)->flag; - ++i; + (*i_iter)->missing = (*i_iter)->flag; + ++i_iter; } //////////////////////////////////////////////// --- plink-1.07.orig/elf.cpp +++ plink-1.07/elf.cpp @@ -1175,10 +1175,10 @@ << setw(8) << gcnt << " " << setw(8) << (double)cnt / (double)gcnt << "\n"; - map::iterator i = chr_cnt.begin(); - while ( i != chr_cnt.end() ) + map::iterator i_iter = chr_cnt.begin(); + while ( i_iter != chr_cnt.end() ) { - int c = i->first; + int c = i_iter->first; int x = chr_cnt.find( c )->second; int y = chr_gcnt.find( c )->second; @@ -1189,7 +1189,7 @@ << setw(8) << y << " " << setw(8) << (double)x / (double)y << "\n"; - ++i; + ++i_iter; } } --- plink-1.07.orig/idhelp.cpp +++ plink-1.07/idhelp.cpp @@ -772,12 +772,12 @@ for (int j = 0 ; j < jointField.size(); j++ ) { set & jf = jointField[j]; - set::iterator j = jf.begin(); + set::iterator j_iter = jf.begin(); PP->printLOG(" { "); - while ( j != jf.end() ) + while ( j_iter != jf.end() ) { - PP->printLOG( (*j)->name + " " ); - ++j; + PP->printLOG( (*j_iter)->name + " " ); + ++j_iter; } PP->printLOG(" }"); } debian/patches/30_endiandetection.patch0000644000000000000000000000252011204171270015267 0ustar Author: Peter Green Puropose: Fallback to endian.h if all else fails on 64bit machines Closes: #528659 Forwarded: Shaun Purcell License: same as plink itself. =================================================================== --- plink-1.06.orig/Rsrv.h 2009-05-15 03:35:29.000000000 +0100 +++ plink-1.06/Rsrv.h 2009-05-15 03:35:41.000000000 +0100 @@ -313,7 +313,18 @@ #define __BIG_ENDIAN__ 1 #define SWAPEND 1 #elif ! defined Win32 /* Windows is little-endian is most cases, anywhere else we're stuck */ -#error "Cannot determine endianness. Make sure config.h is included or __{BIG|LITTLE}_ENDIAN__ is defined ." + //try endian.h before we finally bail out + #include + #if __BYTE_ORDER == __LITTLE_ENDIAN + #warning using little endian based on information from endian.h + #define __LITTLE_ENDIAN__ 1 + #elif __BYTE_ORDER == __BIG_ENDIAN + #warning using big endian based on information from endian.h + #define __BIG_ENDIAN__ 1 + #define SWAPEND 1 + #else + #error "Cannot determine endianness. Make sure config.h is included or __{BIG|LITTLE}_ENDIAN__ is defined ." + #endif #endif /* FIXME: all the mess below needs more efficient implementation - the current one is so messy to work around alignment problems on some platforms like Sun and HP 9000 */ debian/patches/series0000644000000000000000000000004711745174071012042 0ustar 30_endiandetection.patch gcc-4.7.patch debian/README.Debian0000644000000000000000000000306611176406110011231 0ustar plink for Debian ---------------- plink is a very fine piece of software and the world should thank the authors for their efforts. plink knows how to interact with gplink and haploview. The packaging of the latter is already being prepared. The prior still seeks a maintainer. Users of plink may also be interested in other packages the that Debian-Med.alioth.debian.org community has brought ot Debian, e.g. r-cran-qtl and general packages for bioinformatics research. Name conflict with plink from ssh clone putty ============================================= At http://bugs.debian.org/503367 you can read the full discussion about a name clash between one component of the frequently used ssh software putty and plink. The short story is: We are facing a name clash in the Free Software universe and we have to circumvent this somehow. Following the arguing in the bug discussion the plink package has to do the name change. So we found the following solution: 1. The plink executable will be copied to /usr/lib/plink/plink 2. A symlink /usr/bin/p-link points to this location. So if you want to use plink with its original name just do the following: Set the PATH variable like export PATH="/usr/lib/plink:$PATH" or alternatively set a symlink into a directory which is normally in your PATH anyway like ln -s /usr/lib/plink/plink /usr/local/bin/plink if /usr/local/bin is in your PATH. This makes sure that scripts you are using will find the correct plink executable. -- Andreas Tille Tue, 31 Mar 2009 22:28:25 +0200 debian/plink.install0000644000000000000000000000002411164655640011677 0ustar plink usr/lib/plink debian/manpages0000644000000000000000000000001311164656715010712 0ustar debian/*.1 debian/watch0000644000000000000000000000011511110210474010203 0ustar version=3 http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-(.*)-src.zip debian/plink.links0000644000000000000000000000004311176406323011345 0ustar usr/lib/plink/plink usr/bin/p-link debian/dirs0000644000000000000000000000001011110210474010030 0ustar usr/bin debian/NEWS.Debian0000644000000000000000000000143311176405746011062 0ustar Name conflict with plink from ssh clone putty ============================================= We are facing a name clash in the Free Software universe and we have to circumvent. 1. The plink executable will be copied to /usr/lib/plink/plink 2. A symlink /usr/bin/p-link points to this location. So if you want to use plink with its original name just do the following: Set the PATH variable like export PATH="/usr/lib/plink:$PATH" or alternatively set a symlink into a directory which is normally in your PATH anyway like ln -s /usr/lib/plink/plink /usr/local/bin/plink if /usr/local/bin is in your PATH. This makes sure that scripts you are using will find the correct plink executable. -- Andreas Tille Tue, 31 Mar 2009 22:28:25 +0200 debian/changelog0000644000000000000000000000624311745210541011045 0ustar 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 -- Andreas Tille Mon, 23 Apr 2012 07:23:07 +0000 plink (1.07-2) unstable; urgency=low * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Removed quilt from Build-Depends * debian/upstream: Added citation information * debian/source/format: 3.0 (quilt) * debian/get-orig-source: Better chances to get a unique upstream tarball after repackaging * debian/copyright: - Rewritten to match DEP5 and verified using cme fix dpkg-copyright - Fix FSF address * debian/rules: Rewritten to use short dh * debian/patches/gcc-4.7.patch: Fix nested declaration Thanks for the hints on debian-mentors list to Rodolfo García Peñas , Dmitry Nezhevenko , Fernando Lemos Sun, 22 Apr 2012 18:55:34 +0200 plink (1.07-1) unstable; urgency=low * New upstream version * Removed debian/patches/20_plink-1.06-gcc4.4.patch because it is applied upstream * Standards-Version: 3.8.3 (no changes needed) * Debhelper 7 * Build-Depends: zlib1g-dev -- Andreas Tille Fri, 23 Oct 2009 13:35:02 +0200 plink (1.06-4) unstable; urgency=low * debian/rules: - Add support for DEB_BUILD_OPTIONS (Policy § 4.9.1). - Set FORCE_DYNAMIC=1 instead of patching the Makefile (deleted debian/patches/dynamic.patch). * debian/control: - Added myself to the uploaders. - Incremented Standards-Version to reflect conformance with Policy 3.8.2 (no changes needed). * documented in README.source how to find help with quilt. -- Charles Plessy Wed, 15 Jul 2009 08:08:15 +0900 plink (1.06-3) unstable; urgency=low * Now really applying the patch to fix 64bit problems which really Closes: #528659 -- Andreas Tille Tue, 19 May 2009 08:11:21 +0200 plink (1.06-2) unstable; urgency=low * Fallback to endian.h if all else fails on 64bit machines (Thanks to Peter Green for the patch) Closes: #528659 -- Andreas Tille Sat, 16 May 2009 21:19:32 +0200 plink (1.06-1) unstable; urgency=low * New upstream version * debian/get-orig-source * Standards-Version: 3.8.1 (no changes needed) * Moved plink executable to /usr/lib/plink and symlinked /usr/bin/p-link to this location; renamed manpage accordingly Added explicit hint in README.Debian how to proceed if you need the original name. Closes: #503367 * debian/patches/20_plink-1.06-gcc4.4.patch: Patch to compile using gcc 4.4 * debian/rules: Make sure example data files are not executable * debian/patches/dynamic.patch: do not link statically -- Andreas Tille Mon, 04 May 2009 10:17:04 +0200 plink (1.03p1-1) unstable; urgency=low * Initial release (Closes: #490832). -- Steffen Moeller Sun, 24 Aug 2008 17:10:55 +0200 debian/rules0000755000000000000000000000107011745051354010251 0ustar #!/usr/bin/make -f # -*- makefile -*- pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') CXXFLAGS := -Wall $(shell dpkg-buildflags --get CXXFLAGS) CXXFLAGS += -DWITH_R_PLUGINS # This would be added by Upstream makefile, but we override CXXFLAGS… CXXFLAGS += -DUNIX %: dh $@ override_dh_auto_clean: dh_auto_clean rm -f plink override_dh_auto_build: $(MAKE) CXXFLAGS='$(CXXFLAGS)' FORCE_DYNAMIC=1 override_dh_installexamples: dh_installexamples chmod 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/* get-orig-source: . debian/get-orig-source