[med-svn] r3339 - trunk/packages/plink/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu Apr 30 20:57:26 UTC 2009
Author: tille
Date: 2009-04-30 20:57:26 +0000 (Thu, 30 Apr 2009)
New Revision: 3339
Added:
trunk/packages/plink/trunk/debian/NEWS.Debian
trunk/packages/plink/trunk/debian/p-link.1
Removed:
trunk/packages/plink/trunk/debian/patches/
trunk/packages/plink/trunk/debian/snplink.1
Modified:
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/plink.links
trunk/packages/plink/trunk/debian/rules
Log:
Adapt to new upstream version which has applied Debian patches; the rename of plink is not done to snplink but to p-link
Added: trunk/packages/plink/trunk/debian/NEWS.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/NEWS.Debian (rev 0)
+++ trunk/packages/plink/trunk/debian/NEWS.Debian 2009-04-30 20:57:26 UTC (rev 3339)
@@ -0,0 +1,26 @@
+Name conflict with plink from ssh clone putty
+=============================================
+
+We are facing a name clash in the Free Software universe and we have
+to circumvent.
+
+ 1. The plink executable will be copied to
+ /usr/lib/plink/plink
+ 2. A symlink
+ /usr/bin/p-link
+ points to this location.
+
+So if you want to use plink with its original name just do the
+following: Set the PATH variable like
+
+ export PATH="/usr/lib/plink:$PATH"
+
+or alternatively set a symlink into a directory which is normally in
+your PATH anyway like
+
+ ln -s /usr/lib/plink/plink /usr/local/bin/plink
+
+if /usr/local/bin is in your PATH. This makes sure that scripts you
+are using will find the correct plink executable.
+
+ -- Andreas Tille <tille at debian.org> Tue, 31 Mar 2009 22:28:25 +0200
Modified: trunk/packages/plink/trunk/debian/README.Debian
===================================================================
--- trunk/packages/plink/trunk/debian/README.Debian 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/README.Debian 2009-04-30 20:57:26 UTC (rev 3339)
@@ -25,7 +25,7 @@
1. The plink executable will be copied to
/usr/lib/plink/plink
2. A symlink
- /usr/bin/snplink
+ /usr/bin/p-link
points to this location.
So if you want to use plink with its original name just do the
Modified: trunk/packages/plink/trunk/debian/README.source
===================================================================
--- trunk/packages/plink/trunk/debian/README.source 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/README.source 2009-04-30 20:57:26 UTC (rev 3339)
@@ -1,6 +1,4 @@
-Mark of the ftpmasters has requested the gPLINK.jar to disappear. This
-seems like a rightous request of his since that file is produced by an
-independent package that still waits to be packaged.
+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
Modified: trunk/packages/plink/trunk/debian/changelog
===================================================================
--- trunk/packages/plink/trunk/debian/changelog 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/changelog 2009-04-30 20:57:26 UTC (rev 3339)
@@ -1,4 +1,4 @@
-plink (1.05-1) unstable; urgency=low
+plink (1.06-1) unstable; urgency=low
* New upstream version
* debian/get-orig-source
@@ -6,10 +6,12 @@
* Applied gcc4.3 patch from gentoo (Thanks to Andrey Kislyuk
<weaver at gentoo.org>)
* Moved plink executable to /usr/lib/plink and symlinked
- /usr/bin/snplink to this location; renamed manpage accordingly
+ /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/* - removed because applied upstream
+ * removed quilt dependency which is not needed any more
-- Andreas Tille <tille at debian.org> Tue, 31 Mar 2009 22:28:25 +0200
Modified: trunk/packages/plink/trunk/debian/control
===================================================================
--- trunk/packages/plink/trunk/debian/control 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/control 2009-04-30 20:57:26 UTC (rev 3339)
@@ -4,7 +4,7 @@
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>
-Build-Depends: debhelper (>= 5), quilt
+Build-Depends: debhelper (>= 5)
Standards-Version: 3.8.1
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/
@@ -25,3 +25,7 @@
association with the disease phenotypes. The joint
investigation of copy number variations is supported.
A variety of statistical tests have been implemented.
+ .
+ Please note: The executable was renamed to p-link
+ because of a name clash. Please read more about this
+ in /usr/share/doc/README.Debian.
Added: trunk/packages/plink/trunk/debian/p-link.1
===================================================================
--- trunk/packages/plink/trunk/debian/p-link.1 (rev 0)
+++ trunk/packages/plink/trunk/debian/p-link.1 2009-04-30 20:57:26 UTC (rev 3339)
@@ -0,0 +1,29 @@
+.\" 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.links
===================================================================
--- trunk/packages/plink/trunk/debian/plink.links 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/plink.links 2009-04-30 20:57:26 UTC (rev 3339)
@@ -1 +1 @@
-usr/lib/plink/plink usr/bin/snplink
+usr/lib/plink/plink usr/bin/p-link
Modified: trunk/packages/plink/trunk/debian/rules
===================================================================
--- trunk/packages/plink/trunk/debian/rules 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/rules 2009-04-30 20:57:26 UTC (rev 3339)
@@ -1,7 +1,7 @@
#!/usr/bin/make -f
# -*- makefile -*-
-include /usr/share/quilt/quilt.make
+# include /usr/share/quilt/quilt.make
build: patch build-stamp
build-stamp:
Deleted: trunk/packages/plink/trunk/debian/snplink.1
===================================================================
--- trunk/packages/plink/trunk/debian/snplink.1 2009-04-30 20:28:39 UTC (rev 3338)
+++ trunk/packages/plink/trunk/debian/snplink.1 2009-04-30 20:57:26 UTC (rev 3339)
@@ -1,29 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.TH SNPLINK 1 "April 8, 2008"
-.SH NAME
-snplink \- whole genome SNP analysis
-.SH SYNOPSIS
-.B snplink --help
-.SH DESCRIPTION
-
-This binary was renamed from plink to snplink 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.
-
-snplink 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 snplink 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).
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