[med-svn] r18570 - trunk/packages/plink/trunk/debian

Dylan Aïssi bob.dybian-guest at moszumanska.debian.org
Tue Jan 13 07:13:51 UTC 2015


Author: bob.dybian-guest
Date: 2015-01-13 07:13:50 +0000 (Tue, 13 Jan 2015)
New Revision: 18570

Added:
   trunk/packages/plink/trunk/debian/plink1.1
Removed:
   trunk/packages/plink/trunk/debian/p-link.1
Modified:
   trunk/packages/plink/trunk/debian/NEWS.Debian
   trunk/packages/plink/trunk/debian/README.Debian
   trunk/packages/plink/trunk/debian/README.source
   trunk/packages/plink/trunk/debian/changelog
   trunk/packages/plink/trunk/debian/control
   trunk/packages/plink/trunk/debian/copyright
   trunk/packages/plink/trunk/debian/plink.install
   trunk/packages/plink/trunk/debian/plink.links
   trunk/packages/plink/trunk/debian/rules
Log:
Change binary name to plink1

Modified: trunk/packages/plink/trunk/debian/NEWS.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/NEWS.Debian	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/NEWS.Debian	2015-01-13 07:13:50 UTC (rev 18570)
@@ -1,26 +1,27 @@
-Name conflict with plink from ssh clone putty
+Name conflict with plink1, plink1.9, plink2 and plink from ssh clone putty
 =============================================
 
 We are facing a name clash in the Free Software universe and we have
-to circumvent.
+to circumvent. To summarize, we have:
 
-  1. The plink executable will be copied to
-        /usr/lib/plink/plink
-  2. A symlink
+  1. The plink1 executable
+        /usr/bin/plink1
+  2. A symbolic link to the plink1 executable
         /usr/bin/p-link
-     points to this location.
+  3. The plink1.9 executable
+        /usr/bin/plink1.9
+  4. The plink2 executable
+        /usr/bin/plink2
+  5. The plink executable (from putty)
+        /usr/bin/plink
 
-So if you want to use plink with its original name just do the
-following:  Set the PATH variable like
+So if you want to use plink1 with its original name just set a
+symlink into a directory which is normally in your PATH anyway like
 
-  export PATH="/usr/lib/plink:$PATH"
+  ln -s /usr/bin/plink1 /usr/local/bin/plink
 
-or alternatively set a symlink into a directory which is normally in
-your PATH anyway like
-
-  ln -s /usr/lib/plink/plink /usr/local/bin/plink
-
 if /usr/local/bin is in your PATH.  This makes sure that scripts you
 are using will find the correct plink executable.
 
  -- Andreas Tille <tille at debian.org>  Tue, 31 Mar 2009 22:28:25 +0200
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Sat, 10 Jan 2015 23:30:46 +0100

Modified: trunk/packages/plink/trunk/debian/README.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/README.Debian	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/README.Debian	2015-01-13 07:13:50 UTC (rev 18570)
@@ -11,34 +11,35 @@
 e.g. r-cran-qtl and general packages for bioinformatics research.
 
 
-Name conflict with plink from ssh clone putty
+Name conflict with plink1, plink1.9, plink2 and plink from ssh clone putty
 =============================================
 
-At http://bugs.debian.org/503367 you can read the full discussion
-about a name clash between one component of the frequently used
-ssh software putty and plink.  The short story is: We are facing a
-name clash in the Free Software universe and we have to circumvent
-this somehow.  Following the arguing in the bug discussion the
-plink package has to do the name change.  So we found the following
-solution:
+At http://bugs.debian.org/503367 and http://bugs.debian.org/771154#25
+you can read the full discussion about a name clash between one
+component of the frequently used ssh software putty and plink. 
+The short story is: We are facing a name clash in the Free Software
+universe and we have to circumvent this somehow.  Following the
+arguing in the bug discussion the plink package has to do the name
+change.  To summarize, we have:
 
-  1. The plink executable will be copied to
-        /usr/lib/plink/plink
-  2. A symlink
+  1. The plink1 executable
+        /usr/bin/plink1
+  2. A symbolic link to the plink1 executable
         /usr/bin/p-link
-     points to this location.
+  3. The plink1.9 executable
+        /usr/bin/plink1.9
+  4. The plink2 executable
+        /usr/bin/plink2
+  5. The plink executable (from putty)
+        /usr/bin/plink
 
-So if you want to use plink with its original name just do the
-following:  Set the PATH variable like
+So if you want to use plink1 with its original name just set a
+symlink into a directory which is normally in your PATH anyway like
 
-  export PATH="/usr/lib/plink:$PATH"
+  ln -s /usr/bin/plink1 /usr/local/bin/plink
 
-or alternatively set a symlink into a directory which is normally in
-your PATH anyway like
-
-  ln -s /usr/lib/plink/plink /usr/local/bin/plink
-
 if /usr/local/bin is in your PATH.  This makes sure that scripts you
 are using will find the correct plink executable.
 
  -- Andreas Tille <tille at debian.org>  Tue, 31 Mar 2009 22:28:25 +0200
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Sat, 10 Jan 2015 23:30:46 +0100

Modified: trunk/packages/plink/trunk/debian/README.source
===================================================================
--- trunk/packages/plink/trunk/debian/README.source	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/README.source	2015-01-13 07:13:50 UTC (rev 18570)
@@ -4,7 +4,7 @@
 Mark of the ftpmasters has requested the gPLINK.jar to disappear.
 
 This removal will be automatically done if you are using the
-    debian/get-orig-source
+    debian/rules get-orig-source
 script to obtain the upstream tarball.
 
 

Modified: trunk/packages/plink/trunk/debian/changelog
===================================================================
--- trunk/packages/plink/trunk/debian/changelog	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/changelog	2015-01-13 07:13:50 UTC (rev 18570)
@@ -6,6 +6,11 @@
   * debian/watch: Enable '+dfsg' suffix in Debian versions
 
   [ Dylan Aïssi ]
+  * Moved plink executable to /usr/bin/plink1 (and symlinked
+    /usr/bin/p-link to this 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

Modified: trunk/packages/plink/trunk/debian/control
===================================================================
--- trunk/packages/plink/trunk/debian/control	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/control	2015-01-13 07:13:50 UTC (rev 18570)
@@ -29,6 +29,6 @@
  investigation of copy number variations is supported.
  A variety of statistical tests have been implemented.
  .
- Please note: The executable was renamed to p-link
+ Please note: The executable was renamed to plink1
  because of a name clash.  Please read more about this
  in /usr/share/doc/README.Debian.

Modified: trunk/packages/plink/trunk/debian/copyright
===================================================================
--- trunk/packages/plink/trunk/debian/copyright	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/copyright	2015-01-13 07:13:50 UTC (rev 18570)
@@ -17,7 +17,7 @@
 Files: debian/*
 Copyright: 2008 Steffen Moeller <moeller at debian.org>
            2009-2012 Andreas Tille <tille at debian.org>
-           2014 Dylan Aïssi <bob.dybian at gmail.com>
+           2014-2015 Dylan Aïssi <bob.dybian at gmail.com>
 License: GPL-2
 
 License: GPL-2

Deleted: trunk/packages/plink/trunk/debian/p-link.1
===================================================================
--- trunk/packages/plink/trunk/debian/p-link.1	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/p-link.1	2015-01-13 07:13:50 UTC (rev 18570)
@@ -1,29 +0,0 @@
-.\"                                      Hey, EMACS: -*- nroff -*-
-.TH P-LINK 1 "April  8, 2008"
-.SH NAME
-p-link \- whole genome SNP analysis
-.SH SYNOPSIS
-.B p-link --help
-.SH DESCRIPTION
-
-This binary was renamed from plink to p-link because there is a name clash
-between this plink and a part of the ssh clone putty.  Please read
-/usr/share/doc/plink/README.Debian to learn more about this.
-
-P-link works on SNP datasets that have already been pre-analysed for
-their reliability and their calling to AA, BB or AB. It finds associations
-with a disease of single SNPs or pairs, determines haplotype blocks or
-retrieves information on SNPs from an online repository.
-
-This manual page must be insufficient. Please use the help option for a
-quick reminder of the options of p-link or turn to its home page with
-the online documentation or the downloadable manual. 
-
-.SH SEE ALSO
-.BR http://pngu.mgh.harvard.edu/~purcell/plink
-
-.SH AUTHOR
-plink was written by Shaun Purcell <plink at chgr.mgh.harvard.edu>
-.PP
-This manual page was written by Steffen Moeller <moeller at debian.org>,
-for the Debian project (but may be used by others).

Modified: trunk/packages/plink/trunk/debian/plink.install
===================================================================
--- trunk/packages/plink/trunk/debian/plink.install	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/plink.install	2015-01-13 07:13:50 UTC (rev 18570)
@@ -1 +1 @@
-plink usr/lib/plink
+plink1 usr/bin

Modified: trunk/packages/plink/trunk/debian/plink.links
===================================================================
--- trunk/packages/plink/trunk/debian/plink.links	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/plink.links	2015-01-13 07:13:50 UTC (rev 18570)
@@ -1 +1 @@
-usr/lib/plink/plink usr/bin/p-link
+usr/bin/plink1 usr/bin/p-link

Copied: trunk/packages/plink/trunk/debian/plink1.1 (from rev 18560, trunk/packages/plink/trunk/debian/p-link.1)
===================================================================
--- trunk/packages/plink/trunk/debian/plink1.1	                        (rev 0)
+++ trunk/packages/plink/trunk/debian/plink1.1	2015-01-13 07:13:50 UTC (rev 18570)
@@ -0,0 +1,29 @@
+.\"                                      Hey, EMACS: -*- nroff -*-
+.TH PLINK1 1 "April  8, 2008"
+.SH NAME
+plink1 \- whole genome SNP analysis
+.SH SYNOPSIS
+.B plink1 --help
+.SH DESCRIPTION
+
+This binary was renamed from plink to plink1 because there is a name clash
+between this plink and a part of the ssh clone putty.  Please read
+/usr/share/doc/plink/README.Debian to learn more about this.
+
+Plink1 works on SNP datasets that have already been pre-analysed for
+their reliability and their calling to AA, BB or AB. It finds associations
+with a disease of single SNPs or pairs, determines haplotype blocks or
+retrieves information on SNPs from an online repository.
+
+This manual page must be insufficient. Please use the help option for a
+quick reminder of the options of plink1 or turn to its home page with
+the online documentation or the downloadable manual. 
+
+.SH SEE ALSO
+.BR http://pngu.mgh.harvard.edu/~purcell/plink
+
+.SH AUTHOR
+plink was written by Shaun Purcell <plink at chgr.mgh.harvard.edu>
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>,
+for the Debian project (but may be used by others).

Modified: trunk/packages/plink/trunk/debian/rules
===================================================================
--- trunk/packages/plink/trunk/debian/rules	2015-01-13 05:28:50 UTC (rev 18569)
+++ trunk/packages/plink/trunk/debian/rules	2015-01-13 07:13:50 UTC (rev 18570)
@@ -17,11 +17,16 @@
 
 override_dh_auto_clean:
 	dh_auto_clean
-	rm -f plink
+	rm -f plink1
 
 override_dh_auto_build:
 	$(MAKE) CXXFLAGS='$(CXXFLAGS)' FORCE_DYNAMIC=1
 
+override_dh_auto_install:
+	# Change binary name
+	mv $(CURDIR)/plink $(CURDIR)/plink1
+	dh_auto_install
+
 override_dh_installexamples:
 	dh_installexamples
 	chmod 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/*




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