[med-svn] r22843 - in trunk/packages/plink/tags: . 1.07-7/debian 1.07-7/debian/patches
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Mon Oct 17 20:02:09 UTC 2016
Author: bob.dybian-guest
Date: 2016-10-17 20:02:08 +0000 (Mon, 17 Oct 2016)
New Revision: 22843
Added:
trunk/packages/plink/tags/1.07-7/
trunk/packages/plink/tags/1.07-7/debian/changelog
trunk/packages/plink/tags/1.07-7/debian/control
trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch
trunk/packages/plink/tags/1.07-7/debian/patches/Fix_spelling_error.patch
trunk/packages/plink/tags/1.07-7/debian/patches/series
trunk/packages/plink/tags/1.07-7/debian/rules
trunk/packages/plink/tags/1.07-7/debian/upstream.changelog
trunk/packages/plink/tags/1.07-7/debian/watch
Removed:
trunk/packages/plink/tags/1.07-7/debian/changelog
trunk/packages/plink/tags/1.07-7/debian/control
trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch
trunk/packages/plink/tags/1.07-7/debian/patches/series
trunk/packages/plink/tags/1.07-7/debian/rules
trunk/packages/plink/tags/1.07-7/debian/watch
Log:
[svn-buildpackage] Tagging plink 1.07-7
Deleted: trunk/packages/plink/tags/1.07-7/debian/changelog
===================================================================
--- trunk/packages/plink/trunk/debian/changelog 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/changelog 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,135 +0,0 @@
-plink (1.07-6) unstable; urgency=medium
-
- * Recommends: med-config (>= 2.1)
- * Update NEWS.Debian and install this file
-
- -- Andreas Tille <tille at debian.org> Sat, 04 Jul 2015 13:44:46 +0200
-
-plink (1.07-5) experimental; urgency=medium
-
- * Also create a manpage in Debian Med name space
-
- -- Andreas Tille <tille at debian.org> Sat, 31 Jan 2015 10:02:28 +0100
-
-plink (1.07-4) experimental; urgency=low
-
- [ Andreas Tille ]
- * debian/copyright: - Add Files-Excluded to document what was removed
- from original source
- * debian/watch: Enable '+dfsg' suffix in Debian versions for future
- upstream version upgrades
- * debian/README.source: removed since redundant
- * debian/get-orig-source: removed since not needed any more
-
- [ Dylan Aïssi ]
- * Moved plink executable to usr/lib/debian-med/bin/plink (and symlinked
- old locations to this new location) in order to prepare cohabitation
- with plink1.9 and plink2; renamed manpage accordingly
- Added explicit hint in README.Debian how to proceed if you
- need the original name.
- * debian/control:
- - Standards-Version: 3.9.6 (no changes needed)
- - Fixed lintian vcs-field-not-canonical
- * debian/rules:
- - Activate hardening
- - Repack using uscan
- * debian/tests: Add autopkgtest
-
- -- Dylan Aïssi <bob.dybian at gmail.com> Thu, 22 Jan 2015 08:00:59 +0100
-
-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 <tille at debian.org> 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 <kix at kix.es>, Dmitry Nezhevenko <dion at inhex.net>,
- Fernando Lemos <fernandotcl at gmail.com
- Closes: 667325
- * Debhelper 9 (control+compat)
-
- -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plugwash at p10link.net> for the patch)
- Closes: #528659
-
- -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Mon, 04 May 2009 10:17:04 +0200
-
-plink (1.03p1-1) unstable; urgency=low
-
- * Initial release (Closes: #490832).
-
- -- Steffen Moeller <moeller at debian.org> Sun, 24 Aug 2008 17:10:55 +0200
-
Copied: trunk/packages/plink/tags/1.07-7/debian/changelog (from rev 22842, trunk/packages/plink/trunk/debian/changelog)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/changelog (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/changelog 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,146 @@
+plink (1.07-7) unstable; urgency=medium
+
+ * Add a patch to fix spelling errors
+ * Install an upstream changelog
+ * Standards-Version: 3.9.8 (no changes needed)
+ * Use secure Vcs-Browser
+ * Set all hardening options
+ * Update uscan options
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Tue, 11 Oct 2016 22:20:19 +0200
+
+plink (1.07-6) unstable; urgency=medium
+
+ * Recommends: med-config (>= 2.1)
+ * Update NEWS.Debian and install this file
+
+ -- Andreas Tille <tille at debian.org> Sat, 04 Jul 2015 13:44:46 +0200
+
+plink (1.07-5) experimental; urgency=medium
+
+ * Also create a manpage in Debian Med name space
+
+ -- Andreas Tille <tille at debian.org> Sat, 31 Jan 2015 10:02:28 +0100
+
+plink (1.07-4) experimental; urgency=low
+
+ [ Andreas Tille ]
+ * debian/copyright: - Add Files-Excluded to document what was removed
+ from original source
+ * debian/watch: Enable '+dfsg' suffix in Debian versions for future
+ upstream version upgrades
+ * debian/README.source: removed since redundant
+ * debian/get-orig-source: removed since not needed any more
+
+ [ Dylan Aïssi ]
+ * Moved plink executable to usr/lib/debian-med/bin/plink (and symlinked
+ old locations to this new location) in order to prepare cohabitation
+ with plink1.9 and plink2; renamed manpage accordingly
+ Added explicit hint in README.Debian how to proceed if you
+ need the original name.
+ * debian/control:
+ - Standards-Version: 3.9.6 (no changes needed)
+ - Fixed lintian vcs-field-not-canonical
+ * debian/rules:
+ - Activate hardening
+ - Repack using uscan
+ * debian/tests: Add autopkgtest
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Thu, 22 Jan 2015 08:00:59 +0100
+
+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 <tille at debian.org> 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 <kix at kix.es>, Dmitry Nezhevenko <dion at inhex.net>,
+ Fernando Lemos <fernandotcl at gmail.com
+ Closes: 667325
+ * Debhelper 9 (control+compat)
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <plugwash at p10link.net> for the patch)
+ Closes: #528659
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Mon, 04 May 2009 10:17:04 +0200
+
+plink (1.03p1-1) unstable; urgency=low
+
+ * Initial release (Closes: #490832).
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 24 Aug 2008 17:10:55 +0200
+
Deleted: trunk/packages/plink/tags/1.07-7/debian/control
===================================================================
--- trunk/packages/plink/trunk/debian/control 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/control 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,37 +0,0 @@
-Source: plink
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>,
- Charles Plessy <plessy at debian.org>,
- Dylan Aïssi <bob.dybian at gmail.com>
-Section: science
-Testsuite: autopkgtest
-Priority: optional
-Build-Depends: debhelper (>= 9),
- zlib1g-dev
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/plink/trunk/
-Vcs-Svn: svn://anonscm.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}
-Recommends: med-config (>= 2.1)
-Description: whole-genome association analysis toolset
- plink expects as input the data from SNP (single
- nucleotide polymorphism) chips of many individuals
- and their phenotypical description of a disease.
- It finds associations of single or pairs of DNA
- variations with a phenotype and can retrieve
- SNP annotation from an online source.
- .
- SNPs can evaluated individually or as pairs for their
- association with the disease phenotypes. The joint
- investigation of copy number variations is supported.
- A variety of statistical tests have been implemented.
- .
- Please note: The executable was renamed to plink1
- because of a name clash. Please read more about this
- in /usr/share/doc/README.Debian.
Copied: trunk/packages/plink/tags/1.07-7/debian/control (from rev 22835, trunk/packages/plink/trunk/debian/control)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/control (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/control 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,37 @@
+Source: plink
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Dylan Aïssi <bob.dybian at gmail.com>
+Section: science
+Testsuite: autopkgtest
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/plink/trunk/
+Vcs-Svn: svn://anonscm.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}
+Recommends: med-config (>= 2.1)
+Description: whole-genome association analysis toolset
+ plink expects as input the data from SNP (single
+ nucleotide polymorphism) chips of many individuals
+ and their phenotypical description of a disease.
+ It finds associations of single or pairs of DNA
+ variations with a phenotype and can retrieve
+ SNP annotation from an online source.
+ .
+ SNPs can evaluated individually or as pairs for their
+ association with the disease phenotypes. The joint
+ investigation of copy number variations is supported.
+ A variety of statistical tests have been implemented.
+ .
+ Please note: The executable was renamed to plink1
+ because of a name clash. Please read more about this
+ in /usr/share/doc/README.Debian.
Deleted: trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch
===================================================================
--- trunk/packages/plink/trunk/debian/patches/30_endiandetection.patch 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,28 +0,0 @@
-Author: Peter Green <plugwash at p10link.net>
-Puropose: Fallback to endian.h if all else fails on 64bit machines
-Closes: #528659
-Forwarded: Shaun Purcell <plink at chgr.mgh.harvard.edu>
-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 <endian.h>
-+ #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 */
Copied: trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch (from rev 22834, trunk/packages/plink/trunk/debian/patches/30_endiandetection.patch)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/patches/30_endiandetection.patch 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,28 @@
+Author: Peter Green <plugwash at p10link.net>
+Puropose: Fallback to endian.h if all else fails on 64bit machines
+Closes: #528659
+Forwarded: Shaun Purcell <plink at chgr.mgh.harvard.edu>
+License: same as plink itself.
+===================================================================
+--- a/Rsrv.h
++++ b/Rsrv.h
+@@ -321,7 +321,18 @@
+ #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 <endian.h>
++ #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 */
Copied: trunk/packages/plink/tags/1.07-7/debian/patches/Fix_spelling_error.patch (from rev 22835, trunk/packages/plink/trunk/debian/patches/Fix_spelling_error.patch)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/patches/Fix_spelling_error.patch (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/patches/Fix_spelling_error.patch 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,65 @@
+Author: Dylan Aïssi
+Description: Fix spelling error.
+Last-Update: 2016-10-11
+
+--- a/dosage.cpp
++++ b/dosage.cpp
+@@ -1258,7 +1258,7 @@
+ + " markers, " + int2str( totCount )
+ + " across all files\n");
+ if ( nonF == 0 )
+- printLOG("All SNPs occured exactly once in all files\n");
++ printLOG("All SNPs occurred exactly once in all files\n");
+ else
+ printLOG("Note: " + int2str(nonF) + " SNPs did not occur exactly once per file\n");
+
+--- a/gvar.cpp
++++ b/gvar.cpp
+@@ -586,7 +586,7 @@
+
+ if ( true )
+ {
+- printLOG("Writing frequency & genotyping informtion to [ "
++ printLOG("Writing frequency & genotyping information to [ "
+ + par::output_file_name
+ + ".gvar.summary ]\n");
+ GOUT.open( ( par::output_file_name
+--- a/model.cpp
++++ b/model.cpp
+@@ -165,7 +165,7 @@
+ void Model::addDominanceSNP(int d)
+ {
+ if ( ! has_snps )
+- error("Cannot add SNP to thie MODEL");
++ error("Cannot add SNP to this MODEL");
+
+ dominance.push_back(d);
+
+--- a/binput.cpp
++++ b/binput.cpp
+@@ -471,10 +471,10 @@
+ // If 0.99 file format
+ if ( (!v1_bfile) && ( b[1] || b[2] || b[3] || b[4] || b[5] || b[6] || b[7] ) )
+ {
+- printLOG("\n *** Possible problem: guessing that BED is < v0.99 *** \n");
+- printLOG(" *** High chance of data corruption, spurious results *** \n");
+- printLOG(" *** Unles you are _sure_ this really is an old BED file *** \n");
+- printLOG(" *** you should recreate PED -> BED *** \n\n");
++ printLOG("\n *** Possible problem: guessing that BED is < v0.99 *** \n");
++ printLOG(" *** High chance of data corruption, spurious results *** \n");
++ printLOG(" *** Unless you are _sure_ this really is an old BED file *** \n");
++ printLOG(" *** you should recreate PED -> BED *** \n\n");
+
+ bfile_SNP_major = false;
+ BIT.close();
+--- a/sets.cpp
++++ b/sets.cpp
+@@ -812,7 +812,7 @@
+ void Set::profileTestInitialise()
+ {
+
+- PP->printLOG("Initalising profile-based set test\n");
++ PP->printLOG("Initialising profile-based set test\n");
+
+ // Set up the mapping to determine which set(s)
+ // a given SNP is in
Deleted: trunk/packages/plink/tags/1.07-7/debian/patches/series
===================================================================
--- trunk/packages/plink/trunk/debian/patches/series 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/patches/series 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,2 +0,0 @@
-30_endiandetection.patch
-gcc-4.7.patch
Copied: trunk/packages/plink/tags/1.07-7/debian/patches/series (from rev 22835, trunk/packages/plink/trunk/debian/patches/series)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/patches/series (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/patches/series 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,3 @@
+30_endiandetection.patch
+gcc-4.7.patch
+Fix_spelling_error.patch
Deleted: trunk/packages/plink/tags/1.07-7/debian/rules
===================================================================
--- trunk/packages/plink/trunk/debian/rules 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/rules 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,30 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-
-CXXFLAGS := -Wall $(shell dpkg-buildflags --get CXXFLAGS 2>/dev/null | sed -e 's/-O2//g')
-CXXFLAGS += -DWITH_R_PLUGINS
-
-# Activate hardening
-CXXFLAGS += $(shell dpkg-buildflags --get CPPFLAGS) $(shell dpkg-buildflags --get LDFLAGS)
-
-# This would be added by Upstream makefile, but we override CXXFLAGS…
-CXXFLAGS += -DUNIX -O3
-
-%:
- 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:
- uscan --verbose --force-download --repack --compress xz
Copied: trunk/packages/plink/tags/1.07-7/debian/rules (from rev 22835, trunk/packages/plink/trunk/debian/rules)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/rules (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/rules 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,31 @@
+#!/usr/bin/make -f
+
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+CXXFLAGS := -Wall $(shell dpkg-buildflags --get CXXFLAGS 2>/dev/null | sed -e 's/-O2//g')
+CXXFLAGS += -DWITH_R_PLUGINS
+
+# Activate hardening
+CXXFLAGS += $(shell dpkg-buildflags --get CPPFLAGS) $(shell dpkg-buildflags --get LDFLAGS)
+
+# This would be added by Upstream makefile, but we override CXXFLAGS…
+CXXFLAGS += -DUNIX -O3
+
+%:
+ 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/*
+
+override_dh_installchangelogs:
+ dh_installchangelogs debian/upstream.changelog
Copied: trunk/packages/plink/tags/1.07-7/debian/upstream.changelog (from rev 22835, trunk/packages/plink/trunk/debian/upstream.changelog)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/upstream.changelog (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/upstream.changelog 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,479 @@
+V1.07 (10-Oct-2009)
+
+ Added --meta-analysis function
+ Added --annotate function
+ Added --dosage, --write-dosage, etc
+ Added --Z-genome and ability to read compressed .genome.gz
+ Added --simulate-qt to simulate quantitative trait data
+ Added --recode-rlist and --recode-lgen/--with-reference
+ Added preliminary ZLIB support for reading and writing compressed files directly
+ Added --standard-beta for --linear
+ Added --counts to modify --assoc output
+ Added dosage-based score analysis
+
+ Changed how options are passed to commands
+ Changed order of --reference-allele and --freq, so that the reference is now fixed prior to calculating and reporting allele frequencies
+ Improved speed of binary file merging
+ MAF-based SNP removal for --indep-pairwise option
+
+ Fixed bug in --blocks routine
+ Fixed bug in --adjust with quantitative trait --assoc
+ Fixed bug in --fisher and --adjust
+ Fixed bug in --set-test with selection of SNPs in LE
+
+V1.06 (24-Apr-2009)
+
+ Added --show-tags and modifiers, including --list-all
+ Added --blocks command
+ Added --hap-logistic and --hap-linear (with support for covariates and permutation)
+ Added --hap-omnibus that modifies --hap-linear and --hap-logistic
+ Add multiple sizes for sliding window (--hap-window 1,2,3)
+ Fixed issue with D' calculation in --ld command
+ Added --inter-chr option
+ Now enable --ci to work with --chap
+
+ Added --id-dict, --id-match, --id-replace, --id-alias, --id-table, --id-lookup, etc
+
+ Added SVD speedup using LAPACK compile-time option
+
+ Added --reference {file} to complement --lfile
+ Added --allele-count and --compound-genotype support for LGEN files
+ Added --attrib and --attrib-indiv options
+ Added --thin command to prune SNPs randomly
+
+ Added --hide-covar option for GLM tests
+
+ Added --make-perm-pheno {N} to create plink.pphe
+
+ Added --cnv-check-no-overlap
+ Fixed bug that stopped --cnv-method2 from working
+
+ Can now make sets on-the-fly; added --write-set option
+ Added --make-set-complement {label}
+ Now added a group field to ranges; added --make-set-collapse-group, --make-set-complement-group
+ Fixed issue when mapping ranges to SNPs, would not properly include all end SNPs
+ Fixed it that --range can take >3 cols (--extract file.txt --range )
+
+ Added --update-pheno (i.e. similar to --pheno, but doesn't set to missing all non-included people
+ Fixed bug in --update-sex and --update-parents
+ Fixed problem with --update-chr
+
+ Changed basic --assoc OR calculation to avoid int size limits in v. large samples
+ Changed --model --perm to only consider ALLELIC, DOM, REC (not GENO)
+
+ Add chr XY for --dog
+ Added --mouse support
+
+ Fixed input to now allow comment lines (starting with #) in MAP files
+ Added --R-port command
+ Skip zero-ing MEs when rel-check/genome mode
+ Add --q-score-range and --q-score-file options to modify --score
+ Added --simulate-haps, and format/error checks for --simulate files
+
+V1.05 (11-Dec-2008)
+
+ Added support for multiple return values from R-plugins; changed basic protocol
+ Added --beta modifier to --logistic, to return beta coefficients, not odds ratios
+ Fixed minor inconsistencies in --cnv-freq-include-exact: now --cnv-freq-exclude-above 1 equals --cnv-freq-include-exact 1 when used with default overlap thresholds
+ Fixed problem with HWE output
+ Added --cnv-test-region option for CNV mapping
+ Added the --subset command to work with --set
+ Changed --clump-best to preferentially take the same SNP
+ Added option to downweight set-based tests with --lambda
+ Added option --reference-allele to specify manually which is reference allele A1, i.e. instead of minor allele
+ Added support for --rice chromosomes
+ Added --ld-snp-list option
+ Added --make-set-collapse
+ Added --update-alleles, --update-chr, --update-name, --update-ids, --update-sex and --update-parents
+ The --pfilter command now works for --mh
+ Fixed problem with the --hap-tdt command (wasn't working in 1.04 at all)
+ Added support for SNP-specific and genotype-specific quality score filters (--qual-scores and --qual-geno-scores, with corresponding commands --qual-threshold and --qual-max-threshold and --qual-geno-threshold and --qual-geno-max-threshold
+ Made default --score behavior to impute missing genotype scores based on sample frequency, unless --score-no-mean-imputation specified
+ Fixed minor issue with --simulation routine (now we do not assume HWE holds within cases and controls, but only in the population as a whole).
+ Output format of .genome file is changed
+ Modified --genome to display the type of relationship, and expected IBD sharing level, if pair are in same family; also changed output format
+ Added --rel-check modifier to --genome, so that only pairs within the same FID code are considered
+ Modified --read-genome option to accept different format .genome files, by looking for header rows rather than assuming fixed column number/order
+ Added --set-table command to make a SNP by SET matrix
+ Added --tucc option to make pseudo case/control units from trio data
+
+V1.04 (26-Aug-2008)
+
+ Added -gene-report function (with --gene-list, etc)
+ Added --cnv-subset option
+ Added --cnv-verbose-report-regions option
+ Added --clump-best, --clump-range and --clump-range-border
+ Added new LD-aware set-based test and functions --set-p, --set-r2
+ Added ability to include --covar with --gvar
+ Added --flip-subset option, to flip strand only for some individuals
+ Added --flip-scan procedure, to identify likely strand-flip errors
+ Added --mperm-save and --mperm-save-all options
+ Now reports sample summary after filtering for QTs, as for case/control data
+ Now --pfilter works on .adjusted output files also
+ Changed default behavior to not set pheotype to missing if sex code is missing
+ Changed --recode, etc, output names to plink.ped, etc, rather than plink.recode.ped
+ Added --must-have-sex option to set phenotype to missing when recoding data
+ Added --make-pheno {file} * feature to set as cases people in {file}, else control
+ N_GENO field is now always reported in the missing data output
+ Added fields PHOM and PHET to .hom output (and modified --read-homozyg also)
+ Added function --compound-genotype to allele AG, 11, 00, etc in PED files only
+ Changed default thresholds (to be similar to --all)
+ Added --output-missing-phenotype and --output-missing-genotype options
+ Added --keep-allele-order to stop flipping of allele codes when minor allele frequency is greater than 0.5
+ Added --proxy-b-r2 to specify alternate proxy parameters for rarer alleles
+ Added allele codes and frequencies to --homog output files
+ Added allele code fields to --hardy and --model output
+ Fixed female Y chromosome genotype rate counting
+ Fixed a problem with --proxy-glm and missing haplotypic data
+ Fixed --R function to send counts of minor, not major, allele
+ Fixed issue with missing genotypes and --gvar association statistics
+ Fixed minor bug with --hardy2 and --hwe2
+ Fixed problem when --sex used with --chap test
+ Fixed problem with --qfam routine when there are no valid observations
+ Fixed a bug with the --score function
+ Fixed a bug with --hap-impute when used on the X chromosome
+ Fixed a bug in the CNV frequency filter commands
+ Corrected mislabelling of distances/similarities for IBM clustering
+ Removed Hotelling's T2 test from this version
+ Updated the --lookup routines; changed the backend server considerably
+ Updated Rserve client code for use with Rserve version 0.5.2
+ Added gene-lists to resources section on web
+ Updated HapMap resource to latest release
+
+V1.03 (10-Jun-2008)
+
+ Added teaching material/tutorial to resources section of web
+ Added --write-cluster, which can handle strings
+ Added --cnv-freq-exclude-exact and --cnv-freq-include-exact
+ Added --cnv-region-overlap
+ Displays type and score display in --segment-group for CNVs
+ Fixed problem with --read-freq
+ Fixed problem with --hethom and X chromosome data
+ Fixed problem when --condition and --genotypic used together
+ Added --genome-minimal and --read-genome-minimal
+ Now possible to --filter on strings and lists of strings
+ Added --make-pheno command to generate a binary phenotype given string filter
+ Allow --keep and --remove files to have additional columns beyond two
+ Additional case/control statistics given in LOG after filtering
+ Fixed a bug in the --hap-tdt and --proxy-tdt analyses
+ Added the --make-set and --make-set-border commands
+ Added --lookup-kb and --lookup-gene-kb
+ Added --lookup-gene-list (to create a SET file)
+ Added additional output information to SNP and gene lookups
+ Added --ld-snp command to modify the behaviour of --r2
+ LD pruning now considers non-autosomal markers
+ Fixed some issues with non-human data and the IBS/IBD calculation (previously skipped chromosomes over 22)
+
+V1.02 (27-Mar-2008)
+
+ Added beta versions of CNV and generic variant commands, described here
+ Created a PDF version of the web page
+ Added --hethom flag to modify --genotypic
+ Added --seed to specify a fixed random seed
+ Added --recode-allele to modify --recodeA
+ Fixed issue with --clump-index-first option
+ Enabled PED files to be input from standard input (--ped -)
+ Fixed potential error in --chap output when test not defined
+
+V1.01 (28-Jan-2008)
+
+ Added --dummy-coding modifier for --write-covar
+ Added --upate-map
+ Outputs phenotype names for --all-pheno if given
+ Reworked --mds-plot and --mds-cluster option to work with --within and without re-running the clustering
+ Fixed --qfam issues with permutation test
+ Changed defaults for --proxy-assoc and --proxy-impute
+ Changed direction of allele coding for proxy association options
+ Changed --proxy-r2-filter command (3 parameters) and naming
+ Changed syntax for proxy association options, --proxy-r2, etc
+ Added --proxy-glm method
+ Fixed problems with --hap-impute
+ Fixed problem with --hap-window
+ Issue with hyphens in SNP names and use as range delimiter (--d)
+ Fixed issue with numeric chromosome codes greater than 22 and --file
+ Changed output format of TDT and CMH commands
+ Make monomorphic SNPs have missing alleles in output if forced
+ Fixed minor problem with --bmerge when more than 2 alleles seen per SNP
+ Physical position output correctly with --genotypic option
+ Changed threshold to print NA in logistic
+ Changed headers BETA or OR in GLM output for clarity
+ Now --recodeA and --recodeAD count number of minor alleles
+ Added --sheep option
+ Fixed problem with --homozyg
+
+V1.00 (4-Dec-2007)
+
+ Added conditional haplotype-based testing (--chap)
+ Added simple data simulation option (--simulate)
+ Added/extended SNP imputation functions (--proxy-assoc and --proxy-impute)
+ Added LD-based results clumping procedure (--clump)
+ Added option to select specific covariates (--values)
+ Added ability to specify lists and ranges of SNPs (--snps)
+ Added ability to select ranges based on regions (--range)
+ Added proxy selection features based on LD (--proxy-r2-filter)
+ Added simple "risk-profile" tool (--score)
+ Fixed issue with scaling of covariates in GLMs
+ Added --rerun option to repeat analysis given LOG file
+ Added --write-snplist option
+ Fixed dirction-of-effect error in haplotypic QTL test
+ Enabled --fisher to work with --model
+ Made variance inflation factor default value less stringent
+ Fixed some problems with haplotype TDT
+ Fixed problem with slightly different p-values for QTL tests from --adjust
+ Fixed bug in --all-pheno option when used with disease traits
+ Fixed bug in --epistasis routine regarding handling of missing data
+
+V0.99s (26-July-2007)
+
+ Added SNP annotation --lookup set of options
+ Added proxy assocition functions (--proxy-assoc, etc)
+ Added extensible R plugin functionality (--R)
+ Added --lfile option for long-format input
+ Fixed problem with all-male or all-female X chromosome test
+ Added r-squared calculation for two SNPs based on haplotype frequencies
+ Added geno-grouping speedup to E-M algorithm; fixed minor problem with treatment of missing genotype data
+ Added --oblig-missing and --oblig-cluster options, to specify obligatory-missing genotypes
+ Added --impute-sex option
+ Added concordance calculation to --merge-mode 6 and 7
+ Added haplotype support for X and haploid chromosomes
+ Added haplotype support for quantitative trait analysis
+ Mendel error filter now zero's out the people implicated as per heurtistic described here
+ Fixed output commands to use user-defined missing phenotype and genotype values
+ Added dominant and recessive models for --linear and --logistic
+ Improved convergence of EM haplotyping routine
+ Fixed minor bug in --parameters function
+ Added --lambda option to fix genomic control factor
+ Added --log10 option to change output in *.adjusted
+ Added --horse species option
+ Added --qq-plot function
+ Added --loop-assoc option
+ Added --distance-matrix option
+ Changed implementation and interface of the --homozyg-* methods
+ Enabled permutation and set-tests with --dfam
+ Added ability to constrain --cluster with --within
+ Added --recode-bimbam, --recode-fastphase and --recode-structure options
+ Fixed minor issue with --het command
+ Added --liability option
+ Fixed issue with --genotypic and --covar
+ Fixed issue with --dfam
+
+V0.99r (29-April-2007)
+
+ Added --parameters and --tests options
+ Added --zero-cluster option
+ Added --no-fid, --no-parents, --no-sex and --no-pheno options
+ Added --with-phenotype flag to modify --write-covar
+ Now give a warning if fileroots contain a fullstop/period character
+ Added --fisher for Fisher's exact test; use this in --test-missing
+ Added --set-test option
+ DFAM can include unrelateds (possibly in clusters) as well as families in a combined test
+ Improved multicollinearity check in linear model tests
+ Added --all-pheno option for some tests
+ Enabled permutation for --mh
+ Added XY and MT chromosome support
+ Fixed problem with --hap-window introduced in 0.99q
+ Fixed --homog for X and changed output format
+ Fixed problem with --out and --script introduced in 0.99q
+
+V0.99q (3-March-2007)
+
+ Support for PED files larger than 4GB
+ Added --tfile to load transposed (row=SNP,column=person) files (i.e. as from --recode --transpose)
+ Added --recodeA option (like --recodeAD but only output additive components)
+ Added --write-covar option and also ability to include covariate files when recoding or making binary files
+ Add simple filters: --filter-cases, --filter-controls, --filter-males, --filter-females, --filter-founders and --filter-nonfounders
+ Added weighted multimarker tests with --whap
+ Added X chromosome and haploid models for --linear and --logistic with --xchr-model
+ Add --set-me-missing -- now, by default, remaining (i.e. for SNPs/individuals not removed) Mendel errors are not fixed to zero when recoding (--make-bed, etc) a file and filtering on --me.
+ Fixed bug in loading of covariates which made missing phenotypes
+ Changed implementation of --fast-epistasis
+ Fixed minor --bmerge issue with monomorphic alleles in offspring-only subsamples
+ Added --allele1234 and --alleleACGT options
+ Fixed CMH output to NA rather than -9
+ Added web-based context-specific warnings
+
+V0.99p (16-January-2007)
+
+ Fixed bug in loading of covariates which made missing phenotypes no longer missing (e.g. -9 phenotype would have been treated literally as -9)
+ Fixed bug in --bmerge function when merged-in SNPs already exist
+ Added --transpose option to modify --recode
+ Fixed bug in --genotypic option that lead to incorrect results
+ Added --test-all option for --linear and --logistic
+ Changed --fast-epistasis to use correlational test
+ Added --ci support for --linear and --logistic
+ Added --mds-plot option
+ Now allow --remove and --keep together (similarly for --extract and --exclude
+ Added --genome-lists option to facilitate parallization of --genome
+ Added lower pool size in pool segment output, with --pool-size option
+ Added odds ratio calculation for --model tests
+ Modified --qfam within test (only model W)
+ Added --check-sex option
+ Cleaned up excessive memory use issue when merging multiple files
+ Added speed-up and bug fixes to QFAM routines
+ Added gPLINK compatibility via --gplink flag
+ Now treats half-missing genotypes, e.g. A 0 as missing rather than giving an error (haploid genotypes should still be coded as homozygous)
+ Recode file options (--make-bed, --recode, etc) now do not automatically set haploid heterozygous genotypes to missing, unless --set-hh-missing specified
+ No longer sets p-values <1e-16 to 0
+ Now use t-statistic for QTL test
+ Improved verbose segmental output (separate files)
+ Added --filter and --mfilter options
+
+V0.99o 27-November-2006
+
+ Permutation applicable to --test-missing option
+ Added --twolocus output option
+ Added --overlap option
+ Added --logistic and --linear options
+ Added --genotypic and --interaction options
+ Reframed --homozyg tests
+ Added epistasis using linear (QT) and logistic regression models
+ Fixed bug in haplotype-based TDT test (counted transmissions to unaffecteds)
+ IBD estimation adjusted, and fixed a minor bug
+
+V0.99n 11-October-2006
+
+ Added option to print warning when duplicate individual or marker IDs are found
+ Added --read-segment option
+ Changed output format of HWE and genotypic/model association tests
+ Implemented new bias-correct IBD estimators
+ Fixed minor bug that could cause problems when merging datasets on some platforms
+ Large restructuring of haplotype inference code
+ Added --test-mishap option
+ Added --indep-pairwise option
+ Added --hap-window option
+ Added --ld-window option
+ Added --plist option
+ Added --read-genome option
+ Added --map3 option
+
+V0.99m 23-August-2006
+
+ Added --gene extraction option
+ Fixed bug affecting labels after set pruning
+ Added --list output option
+ Added --counts option to modify --freq
+ Fixed bug in the Hotelling's T(2) test handling of missing genotypes
+ Added permutation options for --model
+ Fixed minor bug introduced in v0.99l that caused crash when attempting a set-based TDT analysis
+ Altered some field headers in various output files for greater consistency
+
+V0.99l 27-July-2006
+
+ Added --bmerge option to merge in a binary file
+ Added framework for QFAM test (option not yet available in release version)
+ Added Wiggington et al (AJHG, 2005) exact Hardy-Weinberg calculation
+ Added --from-kb etc options to select regions
+
+V0.99j 14-July-2006
+
+ Added --window option to extract a +/- X kb region around a given SNP
+ Fixed bug which made set VIF pruning fail with a set containing a single SNP
+ Redircted ambiguous sex and no-non-missing-founders messages to files (plink.nosex and plink.nof) rather than to plink.log
+ Fixed bug in HWE tests which meant non-founders were included
+
+V0.99i 5-July-2006
+
+ Improved parsing of PED and haplotype specification files; fixed some minor bugs since 0.99h in this regard, mainly DOS versus UNIX issues
+ Fixed bug in haploTDT routine
+ Implemented gene-based canonical correlation test within PLINK (previously, an R script was generated and this analysis was performed externally)
+ Added feature to scan genome and extract a set of SNPs that are relatively uncorrelated with each other (sliding window based on VIF; implemented in the --indep option)
+
+V0.99h 29-June-2006
+
+ Added option to prune SNPs based on LD (i.e. select an independent subset of SNPs) using the --indep option
+ Fixed bug that occurred when creating a binary map file if a SNP had no non-missing alleles (i.e. previously one allele field was left blank, meaning that the file would not be properly read in subsequently)
+ Improved Hotelling's T(2) calculation -- now it better handles highly or completely correlated SNPs
+ Added singular value decomposition routines and variance inflation calculation
+ Add --allow-no-sex option to differently handle individuals with ambiguous sex codes
+ Fixed bug in --r and --r2 routines
+
+V0.99g 20-June-2006
+
+ Implemented web-based version checking
+ Fixed error in which families counted twice when filtering on Mendel errors and performing TDT also
+ Added column count check for PED files
+ Allowed comments in PED files (lines starting #) for basic input and merge commands
+ Fixed specification of --gap for case-only epistasis tests -- using kb now, not bp
+
+V0.99f 12-June-2006
+
+ Fixed bug that TDT in version 0.99e (but not prior versions), that meant that transmissions to unaffecteds as well as affecteds were counted
+ Improved parsing of --merge-list for end-of-file
+
+V0.99e 9-June-2006
+
+ Improved efficiency of haplotype phase routine
+ Added nearest neighbour identification in --neighbour routine, and fixed a minor bug
+ Added support for haplotypic TDT test
+ Fixed error in homozygosity-run analysis
+ Fixed error in handling of monomorphic variants when creating a binary map file
+ Added --snp option to select single SNPs
+ Added out-of-memory warning
+
+V0.99c 23-May-2006
+
+ Fixed error in conversion from SNP-major to individual-major data representations that effected Mendel error check routines
+
+V0.99b 16-May-2006
+
+ Fixed error in Hardy-Weinberg calculations for quantitative traits
+ Implemented --nudge and --impossible features for IBD calculation
+
+V0.99 30-Apr-2006
+
+ Major internal restructuring to hold data in either row-major or column-major formats, depending on choice of analysis (i.e. order genotypes either by individual or by SNP in memory).
+ Added ability to stratify summary statistics by a cluster variable
+ Improved parsing of haplotypes ( creates .mishap file for mis-specified haplotypes)
+ Fixed bug in CMH tests (problem with individuals who were not assigned to a cluster)
+ Fixed problem with extracting SNPs and individuals with binary PED files
+
+V0.98 19-Apr-2006
+
+ Added support for adjusted significance test calculation (Bonferroni, FDR, Sidak, etc)
+ Added --script feature to allow long command lines
+ Added --1 feature to allow for 0/1 coding of affection variables
+ Added --tab feature to control field delimiters in recoded PED files
+ Added proper support for combined label-swapping and gene-dropping permutation (--swap-parents, --swap-sibs and --swap-unrel
+ Corrected bug in filters for binary files that aren't in genomic order (i.e. those that result from merge operations).
+
+V0.97 10-Apr-2006
+
+ Added Hotelling's T2 test for multilocus SNP data
+ Added a test for interaction with quantitative traits and a dichotomous covariate
+ Added --merge-list option to merge more than two filesets simultaneously
+ Fixed bug quantitative trait association test (not dealing with missing phenotypes properly)
+ Fixed some minor bugs with parsing the command line
+
+V0.96 30-Mar-2006
+
+ Fixed bug in --remove option
+ Added Breslow-Day test of homogeneous odds ratios
+ Added option to skip nearby SNPs in case-only epistasis test
+ Added time/date stamps to output
+ Records output in *.log file; most remaining output echoed to STDOUT instead of STDERR (aside from errors and warnings)
+ Improved parsing of command lines (checking numeric inputs, etc)
+ Added -mcc option to specify number of cases:controls in clustering, e.g. for 3:1 matching of cases to controls, for example.
+
+V0.95 20-Mar-2006
+
+ Added Cochran-Mantel-Haenszel tests (2x2xK and IxJxK)
+ Added homogeneity of odds ratio between clusters test (partitioning chi-square)
+ Added support for gene-dropping simulation
+
+V0.94 7-Mar-2006
+
+ Added feature to perform error checking of command line options (scan for unused options)
+ Ability to include external matching criteria for --cluster added
+ Ability to specify merge modes and a diff function for PED files
+
+V0.93 1-Mar-2006
+
+ X chromosome support added for basic association test & quantitative traits
+ Threshold for --genome output based on pi-hat exceeding --min
+
+V0.92 22-Feb-2006
+
+ X chromosome support added for case/control tests, quantitative trait association, TDT, genotypic correlations, allele frequency statistics. Not yet implemented for the population stratification, inbreeding or epistasis tests.
+ --chr and --from X and --to X options added
+ Some problems with the --merge option corrected
+ Now only considers founders for the allele frequency and HWE tests
\ No newline at end of file
Deleted: trunk/packages/plink/tags/1.07-7/debian/watch
===================================================================
--- trunk/packages/plink/trunk/debian/watch 2016-10-11 15:22:59 UTC (rev 22833)
+++ trunk/packages/plink/tags/1.07-7/debian/watch 2016-10-17 20:02:08 UTC (rev 22843)
@@ -1,3 +0,0 @@
-version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
- http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-(\d\S*)-src.zip
Copied: trunk/packages/plink/tags/1.07-7/debian/watch (from rev 22835, trunk/packages/plink/trunk/debian/watch)
===================================================================
--- trunk/packages/plink/tags/1.07-7/debian/watch (rev 0)
+++ trunk/packages/plink/tags/1.07-7/debian/watch 2016-10-17 20:02:08 UTC (rev 22843)
@@ -0,0 +1,3 @@
+version=3
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-(\d\S*)-src.zip
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