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 <[email protected]> Tue, 31 Mar 2009 22:28:25 +0200
+ -- Dylan Aïssi <[email protected]> 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 <[email protected]> Tue, 31 Mar 2009 22:28:25 +0200
+ -- Dylan Aïssi <[email protected]> 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 <[email protected]>
2009-2012 Andreas Tille <[email protected]>
- 2014 Dylan Aïssi <[email protected]>
+ 2014-2015 Dylan Aïssi <[email protected]>
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 <[email protected]>
-.PP
-This manual page was written by Steffen Moeller <[email protected]>,
-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 <[email protected]>
+.PP
+This manual page was written by Steffen Moeller <[email protected]>,
+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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