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 <ti...@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 <ti...@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.dyb...@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 <ti...@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 <k...@kix.es>, Dmitry Nezhevenko <d...@inhex.net>,
-    Fernando Lemos <fernando...@gmail.com
-    Closes: 667325
-  * Debhelper 9 (control+compat)
-
- -- Andreas Tille <ti...@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 <ti...@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 <ple...@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 <ti...@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 <plugw...@p10link.net> for the patch)
-    Closes: #528659
-
- -- Andreas Tille <ti...@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 <ti...@debian.org>  Mon, 04 May 2009 10:17:04 +0200
-
-plink (1.03p1-1) unstable; urgency=low
-
-  * Initial release (Closes: #490832).
-
- -- Steffen Moeller <moel...@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.dyb...@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 <ti...@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 <ti...@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.dyb...@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 <ti...@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 <k...@kix.es>, Dmitry Nezhevenko <d...@inhex.net>,
+    Fernando Lemos <fernando...@gmail.com
+    Closes: 667325
+  * Debhelper 9 (control+compat)
+
+ -- Andreas Tille <ti...@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 <ti...@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 <ple...@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 <ti...@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 <plugw...@p10link.net> for the patch)
+    Closes: #528659
+
+ -- Andreas Tille <ti...@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 <ti...@debian.org>  Mon, 04 May 2009 10:17:04 +0200
+
+plink (1.03p1-1) unstable; urgency=low
+
+  * Initial release (Closes: #490832).
+
+ -- Steffen Moeller <moel...@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-packag...@lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moel...@debian.org>,
-           Andreas Tille <ti...@debian.org>,
-           Charles Plessy <ple...@debian.org>,
-           Dylan Aïssi <bob.dyb...@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-packag...@lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moel...@debian.org>,
+           Andreas Tille <ti...@debian.org>,
+           Charles Plessy <ple...@debian.org>,
+           Dylan Aïssi <bob.dyb...@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 <plugw...@p10link.net>
-Puropose: Fallback to endian.h if all else fails on 64bit machines
-Closes: #528659
-Forwarded: Shaun Purcell <pl...@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 <plugw...@p10link.net>
+Puropose: Fallback to endian.h if all else fails on 64bit machines
+Closes: #528659
+Forwarded: Shaun Purcell <pl...@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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