[med-svn] r1643 - in trunk/packages/loki/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Fri Mar 21 13:39:52 UTC 2008
Author: tille
Date: 2008-03-21 13:39:52 +0000 (Fri, 21 Mar 2008)
New Revision: 1643
Added:
trunk/packages/loki/trunk/debian/loki.manpages
trunk/packages/loki/trunk/debian/patches/
trunk/packages/loki/trunk/debian/patches/10_utils.patch
trunk/packages/loki/trunk/debian/patches/series
Removed:
trunk/packages/loki/trunk/debian/check_het.1
trunk/packages/loki/trunk/debian/hist.1
trunk/packages/loki/trunk/debian/loki_count.1
trunk/packages/loki/trunk/debian/loki_dist.1
trunk/packages/loki/trunk/debian/loki_ext.1
trunk/packages/loki/trunk/debian/loki_freq.1
trunk/packages/loki/trunk/debian/loki_sort_error.1
trunk/packages/loki/trunk/debian/menu
trunk/packages/loki/trunk/debian/prep.1
trunk/packages/loki/trunk/debian/qavg.1
trunk/packages/loki/trunk/debian/watch
Modified:
trunk/packages/loki/trunk/debian/changelog
trunk/packages/loki/trunk/debian/compat
trunk/packages/loki/trunk/debian/control
trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq
trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual
trunk/packages/loki/trunk/debian/loki.1
trunk/packages/loki/trunk/debian/rules
Log:
Preparation of next upload.
Modified: trunk/packages/loki/trunk/debian/changelog
===================================================================
--- trunk/packages/loki/trunk/debian/changelog 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/changelog 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,3 +1,24 @@
+loki (2.4.7.4-2) unstable; urgency=low
+
+ * Debhelper 5
+ * Standards-Version: 3.7.3 (no changes necessary)
+ * Switch to cdbs
+ * Use quilt and patches
+ * Removed [Biology] from short description
+ * Added hint to long description that the project is dead
+ and homepage vanished
+ * Group maintenance according to Debian-Med policy
+ * Added Vcs-Fields
+ * Added Homepage tag (with download page of latest upstream source,
+ upstream seems to be dead since 1995)
+ * Removed watch file because project is dead upstream so watch
+ makes no sense
+ * Use a single manpage and symlinks instead of several copies of the
+ very same manpage file
+ * Remove menu entry that just calls man loki
+
+ -- Andreas Tille <tille at debian.org> Thu, 20 Mar 2008 14:39:11 +0100
+
loki (2.4.7.4-1) unstable; urgency=low
* New upstream release
Deleted: trunk/packages/loki/trunk/debian/check_het.1
===================================================================
--- trunk/packages/loki/trunk/debian/check_het.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/check_het.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/loki/trunk/debian/compat
===================================================================
--- trunk/packages/loki/trunk/debian/compat 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/compat 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1 +1 @@
-4
+5
Modified: trunk/packages/loki/trunk/debian/control
===================================================================
--- trunk/packages/loki/trunk/debian/control 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/control 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,29 +1,34 @@
Source: loki
Section: science
Priority: optional
-Maintainer: Carleos Artime <carleos at uniovi.es>
-Build-Depends: debhelper (>> 4.0.0)
-Standards-Version: 3.6.1
-XBCS-URL: http://loki.homeunix.net
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>,
+ Carleos Artime <carleos at uniovi.es>
+Build-Depends: cdbs, debhelper (>= 5.0), quilt
+Standards-Version: 3.7.3
+Homepage: http://loki.homeunix.net
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/loki/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/loki/trunk/
Package: loki
Architecture: any
Depends: ${shlibs:Depends}
Suggests: loki-doc
-Description: [Biology] MCMC linkage analysis on general pedigrees
+Description: MCMC linkage analysis on general pedigrees
Performs Markov chain Monte Carlo multipoint linkage analysis on large,
complex pedigrees. The current package supports analyses on quantitative
traits only, although this restriction will be lifted in later versions.
Joint estimation of QTL number, position and effects uses Reversible Jump
MCMC. It is also possible to perform affected only IBD sharing analyses.
.
- Homepage: http://loki.homeunix.net.
+ The homepage of this project used to be at http://loki.homeunix.net
+ but the project is dead now and the homepage vanished. The Homepage
+ field above points to the web archive.
Package: loki-doc
Architecture: all
Suggests: loki
-Description: [Biology] Postscript manual for loki
+Description: Postscript manual for loki
Documentation on how to use Simon Heath's "prep" and "loki" tools
for MCMC genetic linkage and IBD analysis on general pedigrees.
- .
- Homepage: http://loki.homeunix.net.
Deleted: trunk/packages/loki/trunk/debian/hist.1
===================================================================
--- trunk/packages/loki/trunk/debian/hist.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/hist.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokifaq 2008-03-21 13:39:52 UTC (rev 1643)
@@ -3,8 +3,7 @@
Author: Simon C. Heath
Abstract: This document answers frequently
asked questions about Loki.
-Section: Apps/Science
+Section: Science/Biology
Format: postscript
-Files: /usr/share/doc/loki/docs/loki_faq.ps.gz
-
+Files: /usr/share/doc/loki-doc/loki_faq.ps.gz
Modified: trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual
===================================================================
--- trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki-doc.doc-base.lokimanual 2008-03-21 13:39:52 UTC (rev 1643)
@@ -4,8 +4,7 @@
Abstract: This manual describes what loki is
and how it can be used to perform genetic
linkage analyses.
-Section: Apps/Science
+Section: Science/Biology
Format: postscript
-Files: /usr/share/doc/loki/docs/loki_doc.ps.gz
-
+Files: /usr/share/doc/loki-doc/loki_doc.ps.gz
Modified: trunk/packages/loki/trunk/debian/loki.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -50,9 +50,7 @@
Show version of the program.
.SH SEE ALSO
The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/.
+.IR /usr/share/doc/loki/.
.SH AUTHOR
This manual page was written by Carleos Artime <carleos at uniovi.es>,
for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/loki/trunk/debian/loki.manpages
===================================================================
--- trunk/packages/loki/trunk/debian/loki.manpages (rev 0)
+++ trunk/packages/loki/trunk/debian/loki.manpages 2008-03-21 13:39:52 UTC (rev 1643)
@@ -0,0 +1 @@
+debian/loki.1
Deleted: trunk/packages/loki/trunk/debian/loki_count.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_count.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki_count.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/loki_dist.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_dist.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki_dist.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/loki_ext.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_ext.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki_ext.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/loki_freq.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_freq.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki_freq.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/loki_sort_error.1
===================================================================
--- trunk/packages/loki/trunk/debian/loki_sort_error.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/loki_sort_error.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/menu
===================================================================
--- trunk/packages/loki/trunk/debian/menu 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/menu 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,2 +0,0 @@
-?package(loki):needs="text" section="Apps/Science"\
- title="loki" command="man loki"
Added: trunk/packages/loki/trunk/debian/patches/10_utils.patch
===================================================================
--- trunk/packages/loki/trunk/debian/patches/10_utils.patch (rev 0)
+++ trunk/packages/loki/trunk/debian/patches/10_utils.patch 2008-03-21 13:39:52 UTC (rev 1643)
@@ -0,0 +1,423 @@
+--- loki.orig/utils/Makefile.in
++++ loki/utils/Makefile.in
+@@ -18,7 +18,7 @@
+
+ SRC = qavg.c hist.c
+ PROGS = qavg hist
+-SCRIPTS = loki_ext count dist freq sort_error
++SCRIPTS = ext count dist freq sort_error
+
+ all: qavg hist
+
+@@ -30,11 +30,11 @@
+
+ ../bin:
+ mkdir ../bin
+-
++
+ scripts: ../bin
+ for file in $(SCRIPTS); do \
+- $(SED) 's!+PERLPROG+!$(PERL)!' $$file.in > $(bindir)/$$file.pl; \
+- $(CHMOD) $(INSTALL_PERM) $(bindir)/$$file.pl; \
++ $(SED) 's!+PERLPROG+!$(PERL)!' $$file.in > $(bindir)/loki_$$file; \
++ $(CHMOD) $(INSTALL_PERM) $(bindir)/loki_$$file; \
+ done
+
+ install: $(PROGS) scripts
+@@ -42,16 +42,16 @@
+ $(CP) $$file $(bindir)/; \
+ $(CHMOD) $(INSTALL_PERM) $(bindir)/$$file ; \
+ done
+-
++
+ clean:
+ rm -f *~ *.o *.a *.bak a.out core seedfile depend
+
+ distclean: clean
+- rm -f Makefile *.pl $(PROGS)
++ rm -f Makefile loki_* $(PROGS)
+ rm -rf ../bin
+-
++
+ depend: $(SRC) ../include/config.h
+ @MAKEDEPEND@ -I../include $(DMALLOC_INC) $(SRC)
+ touch depend
+-
++
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
+--- /dev/null
++++ loki/utils/ext.in
+@@ -0,0 +1,373 @@
++#!+PERLPROG+
++#
++# Script to extract columns from loki.out
++#
++# Should work with output from all versions of Loki (up to loki_2.3)
++#
++# Simon Heath - September 2000
++#
++use Getopt::Std;
++use IO::File;
++use POSIX qw(tmpnam);
++use strict;
++my($i,$j,$k,%opt,$file,$hi,$lo,$flag,$out_type,$version,$link_fg,$start,$stop);
++my($lg,%chrom, at map_start, at map_end, at map_length,$sex_map,$model);
++my(@mkchrom, at mkpos, at mkname,$nmk, at col,$n_cov,$max_col,$ngroup);
++my($it_col,$tv_col,$resvar_col,$mean_col,$addvar_col);
++my($mean_set,$mean,$resvar_set,$resvar,$max_col1,$tau_col,$tau_beta,$tau,$tau_mode);
++my($nc,$nqtl,$nqtl1,$line,$iter,$tv,$tv1,$sz,$nrand, at rand_col, at rand_fg,$tmp);
++my(@no_output,$out_col_flag,$adj);
++my($x1,$x2);
++# Chromsome extracted defaults to the first one
++$opt{c}=1;
++getopts('xc:CDf:r:o:i:',\%opt);
++# -r option sets a range of positions on the chromosome to look at
++if($opt{r}) {
++ $tmp=$opt{r};
++ if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)(.*)/) {
++ $lo=$1;
++ $tmp=$2;
++ }
++ if($tmp=~/^[,-:](.*)/) {
++ $tmp=$1;
++ if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)/) {
++ $hi=$1;
++ }
++ }
++ die "Bad -r option\n" if(!defined($hi) && !defined($lo));
++ if(defined($lo) && defined($hi) && $lo>$hi) {
++ $tmp=$lo;
++ $lo=$hi;
++ $hi=$tmp;
++ }
++}
++# -i option sets a range of iterations to consider
++if($opt{i}) {
++ $tmp=$opt{i};
++ if($tmp=~/^([1-9][0-9]*)(.*)/) {
++ $start=$1;
++ $tmp=$2;
++ }
++ if($tmp=~/^[,-:](.*)/) {
++ $tmp=$1;
++ if($tmp=~/^([1-9][0-9]*)/) {
++ $stop=$1;
++ }
++ }
++ die "Bad -i option\n" if(!defined($start) && !defined($stop));
++ if(defined($start) && defined($stop) && $start>$stop) {
++ $tmp=$start;
++ $start=$stop;
++ $stop=$tmp;
++ }
++ $start=1 if(!defined($start));
++}
++
++# Set default number of genetic groups
++$ngroup=1;
++# Used to store columns where to find interesting quantitities
++# -1 means not known
++$it_col=-1; # Iteration count
++$tv_col=-1; # Total genetic variance
++$resvar_col=-1; # Residual variance
++$mean_col=-1; # Grand mean
++$max_col=-1; # No. fixed output columns
++$n_cov=-1; # No. covariate columns
++$ngroup=1; # No. genetic groups
++$tau_col=-1;
++$tau_mode=-1;
++$out_type=-1; # Output type
++# Open output file if specified, otherwise we use STDOUT
++if($opt{o}) {
++ open OFILE,">".$opt{o} or die "Couldn't open output file ",$opt{o},"\n";
++} else {
++ open OFILE,">&STDOUT" or die "Couldn't dup STDOUT\n";
++}
++$sex_map=0;
++$i=$opt{x}+$opt{C}+$opt{D};
++die "Can not specify more that 1 of the options C,D,x at once.\n" if($i>1);
++$opt{x}=1 unless $i;
++$file=$opt{f}?$opt{f}:"loki.out";
++open FILE,$file or die "Could not open file '$file'\n";
++# Go though file
++while(<FILE>) {
++ $line++;
++ if($flag) { # Parse the data portion of the file
++ split;
++ # Iteration number
++ $iter=$_[0];
++ if($opt{i}) {
++ next if($iter<$start);
++ last if(defined($stop) && $iter>$stop);
++ }
++ $nc=@_;
++ next if($nc<$max_col);
++ if($version==-1) {
++ $i=$max_col+$_[6];
++ last if($nc<$max_col);
++ $ngroup=$_[7];
++ } else {$i=$max_col;}
++ $max_col1=$i;
++ if($opt{C}) {
++ for($i=0;$i<$max_col1;$i++) {print OFILE " $_[$i]";}
++ print OFILE "\n";
++ next;
++ }
++ # Total variance
++ $tv1=0; #first get non-genetic variance
++ for($j=0;$j<$nrand;$j++) {
++ if($rand_fg[$j]==2) {
++ $sz=$_[$rand_col[$j]];
++ $tv1+=$sz;
++ }
++ }
++ # Now get genetic variance
++ if($tv_col>=0) {$tv=$_[$tv_col];}
++ else { # Not specified, must calculate
++ $tv=0;
++ for($j=0;$j<$nrand;$j++) {
++ $sz=$_[$rand_col[$j]];
++ $sz*=$sz if($rand_fg[$j]==1);
++ if($rand_fg[$j]!=2) {$tv+=$sz;}
++ }
++ }
++ # Count QTL's
++ $nqtl=0;
++ $nqtl1=0;
++ while($i<$nc) {
++ $lg=$_[$i];
++ die "Illegal linkage group $lg at line $line column ",$i+1,"\n" if($lg && !$chrom{$lg});
++ $i+=1+$sex_map if($lg || !$out_type);
++ $i+=4+$ngroup;
++ if($tv_col<0) {
++ $sz=$_[$i-1];
++ $tv+=$sz*$sz;
++ }
++ $nqtl++;
++ if($lg) {
++ $nqtl1++;
++ }
++ }
++ # If QTL numbers are given, check against what we found
++ if($out_type<2) {
++ die "Mismatch in QTL numbers ($nqtl,$_[1]) at line $line\n" if($nqtl!=$_[1]);
++ die "Mismatch in linked QTL numbers ($nqtl1,$_[2]) at line $line\n" if($nqtl1!=$_[2]);
++ }
++ # Get residual variance
++ if(!$resvar_set) {
++ # Do we know where it is ?
++ if($resvar_col>=0) {$resvar=$_[$resvar_col];}
++ # if not, guess
++ elsif($out_type<2) {$resvar=$_[4];}
++ else {$resvar=$_[2];}
++ }
++ # Total non-genetic variance
++ $tv1+=$resvar;
++ # Print out a 'standard' (across output types) set of columns
++ if($opt{D}) {
++ # Get Mean
++ if(!$mean_set) {
++ if($mean_col>=0) {$mean=$_[$mean_col];}
++ elsif($out_type<2) {$mean=$_[3];}
++ else {$mean=$_[1];}
++ }
++ # get Tau
++ if($tau_col>=0) {$tau=$_[$tau_col];}
++ elsif($tau_mode>=0) {
++ if($tau_mode==2) {$tau=$resvar*$tau_beta;}
++ else {$tau=$tau_beta;}
++ } else {
++ # Must be a very early version, assume that we know where tau is...
++ $tau=$_[5];
++ }
++ print OFILE "$iter $nqtl $nqtl1 $mean $resvar $tau ";
++ printf OFILE "%g",$tv;
++ # Are we on a recent version with all column info?
++ if($out_col_flag) {
++ for($i=1;$i<$max_col1;$i++) {
++ print OFILE " $_[$i]" if(!$no_output[$i]);
++ }
++ # This is more complicated
++ } else {
++ if(!$out_type) {$i=8;}
++ elsif($out_type<2) {$i=6;}
++ else {$i=3};
++ for(;$i<$max_col1;$i++) {
++ print OFILE " $_[$i]";
++ }
++ }
++ print OFILE "\n";
++ # Extract information about linked QTL's
++ } elsif($opt{x} && $nqtl) {
++ # Go through QTL's
++ $i=$max_col1;
++ while($i<$nc) {
++ $lg=$_[$i];
++ if($lg eq $opt{c}) {
++ $j=$i+1;
++ if($lg) {
++ $x1=$_[$j++];
++ $x2=$_[$j++] if($sex_map);
++ }
++ # Select QTL based on linkage group and range
++ if(!$lg || !$opt{r} || ((!defined($lo) || $x1>=$lo) && (!defined($hi) || $x1<=$hi))) {
++ print OFILE $iter;
++ # Print position if linked
++ if($lg) {
++ print OFILE " $x1";
++ print OFILE " $x2" if($sex_map);
++ }
++ for($k=0;$k<2+$ngroup;$k++) {print OFILE " ",$_[$j++];}
++ $sz=$_[$j];
++ print OFILE " $sz";
++ $sz*=$sz;
++ if($tv>0.0) {printf OFILE " %g",$sz/$tv;}
++ else {print OFILE " 0.0";}
++ if(($tv1+$tv)>0.0) {printf OFILE " %g\n",$sz/($tv+$tv1)}
++ else {print OFILE " 0.0\n";}
++ }
++ }
++ $i+=1+$sex_map if($lg || !$out_type);
++ $i+=4+$ngroup;
++ }
++ }
++ # We've reached the end of the header
++ } elsif(/^--*/) {
++ $flag=1;
++ # $max_col will not be set if working with an earlier version
++ if($max_col<0) {
++ # but $n_cov should be set unless ...
++ if($n_cov>=0) {
++ if($out_type<0) {$out_type=1;}
++ $max_col=3+$n_cov;
++ $version=1;
++ if(!$out_type) {$max_col+=5;}
++ elsif($out_type==1) {$max_col+=3;}
++ } else { # ... we are working with a genuine v2.0 copy
++ $out_type=0;
++ $max_col=8;
++ $version=-1;
++ }
++ }
++ } elsif(!$flag) { # First parse the header
++ if(/^Output format: (\d+)/) {
++ $out_type=$1;
++ next;
++ }
++ if(/^Created by loki (\d+).(\d+).(\d+).*:/) {
++ $version=2 if($1>2 || ($1==2 && $2>=3));
++ next;
++ }
++ # Pull out linkage group information if it is there
++ if(/^Linkage groups:$/) {
++ $link_fg=1;
++ next;
++ }
++ if($link_fg==1) {
++ # Check for linkage group names and map lengths
++ if(/(\d+): (.*)$/) {
++ $lg=$1;
++ if($2=~/^(.*) Map range: (.*)/) {
++ $chrom{$lg}=$1;
++ if($2=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)(.*)/) {
++ $map_start[$lg][0]=$1;
++ $map_end[$lg][0]=$1;
++ if($3=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)/) {
++ $map_start[$lg][1]=$1;
++ $map_end[$lg][1]=$1;
++ $sex_map=1;
++ }
++ } else { die "Error reading linkage group map range\n"; }
++ } else {$chrom{$lg}=$1;}
++ } elsif(/^\s+(.+) - ([\d\.]+)\s*([\d\.]*)/) {
++ if(!$opt{c} || $lg eq $opt{c}) {
++ $mkchrom[$nmk]=$lg;
++ $mkpos[$nmk][0]=$2;
++ $mkpos[$nmk][1]=$3;
++ $mkname[$nmk++]=$1;
++ }
++ } else {
++ # Check for total map length
++ if(/^Total Map Length: (.*)$/) {
++ if($1=~/(\d\d*\.?\d*)cM(.*)/) {
++ $map_length[0]=$1;
++ if($2=~/(\d\d*\.?\d*)cM$/) {
++ $map_length[1]=$1;
++ $sex_map=1;
++ }
++ } else { die "Error reading map lengths\n"; }
++ $link_fg=2;
++ next;
++ }
++ }
++ }
++ $model=$1 if(/^Model: (.+)/);
++ if($link_fg<3) {
++ if(/^Output columns:$/) {
++ $link_fg=3;
++ $out_col_flag=1;
++ next;
++ } elsif(/Output covariate data:$/) {
++ $link_fg=4;
++ }
++ } elsif($link_fg>2) {
++ if(/(\d+): (.*)/) {
++ $col[$1]=$2;
++ $tmp=$1-1;
++ if($link_fg==4) {
++ $link_fg=3;
++ if(!$tmp) {$adj=6;}
++ }
++ $tmp+=$adj;
++ if($2 eq "Total genetic variance") {
++ $tv_col=$tmp;
++ $no_output[$tmp]=1;
++ } elsif($2 eq "Additive variance") {
++ $rand_fg[$nrand]=0;
++ $rand_col[$nrand++]=$tmp;
++ } elsif($2=~/^Additional random variance for/) {
++ $rand_fg[$nrand]=2;
++ $rand_col[$nrand++]=$tmp;
++ } elsif($2=~/\S+ size$/) {
++ $rand_fg[$nrand]=1;
++ $rand_col[$nrand++]=$tmp;
++ } elsif($2 eq "Residual variance") {
++ $resvar_col=$tmp;
++ $no_output[$tmp]=1;
++ } elsif($2 eq "Grand mean") {
++ $mean_col=$tmp;
++ $no_output[$tmp]=1;
++ } elsif($2 eq "Tau") {
++ $tau_col=$tmp;
++ $no_output[$tmp]=1;
++ } elsif($2 eq "No. QTL's in model") {
++ $no_output[$tmp]=1;
++ } elsif($2 eq "No. linked QTL's") {
++ $no_output[$tmp]=1;
++ } elsif($2 eq "No. covariate columns") {
++ $no_output[$tmp]=1;
++ } elsif($2 eq "No. genetic groups") {
++ $no_output[$tmp]=1;
++ }
++ } elsif(/No. covariate columns: (\d+)/) {
++ $n_cov=$1;
++ } elsif(/No. fixed output columns: (\d+)/) {
++ $max_col=$1;
++ } elsif(/No. genetic groups: (\d+)/) {
++ $ngroup=$1;
++ } elsif(/^Sex specific map$/) {
++ $sex_map=1;
++ } elsif(/^Residual variance: ([0-9-.]+)/) {
++ $resvar_set=1;
++ $resvar=$1;
++ } elsif(/^Grand mean: ([0-9-.]+)/) {
++ $mean_set=1;
++ $mean=$1;
++ } elsif(/^Tau Mode: ([0-9]+)/) {
++ $tau_mode=$1;
++ } elsif(/^Tau Beta: ([0-9.]+)/) {
++ $tau_beta=$1;
++ }
++ }
++ }
++}
Added: trunk/packages/loki/trunk/debian/patches/series
===================================================================
--- trunk/packages/loki/trunk/debian/patches/series (rev 0)
+++ trunk/packages/loki/trunk/debian/patches/series 2008-03-21 13:39:52 UTC (rev 1643)
@@ -0,0 +1 @@
+10_utils.patch
Deleted: trunk/packages/loki/trunk/debian/prep.1
===================================================================
--- trunk/packages/loki/trunk/debian/prep.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/prep.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/loki/trunk/debian/qavg.1
===================================================================
--- trunk/packages/loki/trunk/debian/qavg.1 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/qavg.1 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,58 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH LOKI 1 "2004-09-24"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-loki \- Reversible jump MCMC linkage analysis in general pedigrees
-.SH SYNOPSIS
-.B prep
-.RI controlfile
-.br
-.B loki
-.RI -v
-.br
-.B loki
-.RI paramfile
-.SH DESCRIPTION
-This manual page documents briefly the
-.B prep
-and
-.B loki
-commands. Other post-hoc analysis scripts are available; please see
-the complete documentation.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has documentation in PostScript format; see below.
-.PP
-.\" TeX users may be more comfortable with the \fB<whatever>\fP and
-.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
-.\" respectively.
-\fBloki\fP, written by Simon C. Heath, implements segregation and linkage
-analysis on possibly large and complex pedigrees, by means of a Reversible
-Jump Markov Chain Monte Carlo technique.
-\fBprep\fP performs previous data preparation.
-.SH OPTIONS
-.TP
-.B \-v
-Show version of the program.
-.SH SEE ALSO
-The programs are documented fully in
-.IR /usr/share/doc/loki/,
-available on-line at
-.IR http://loki.homeunix.net/ .
-.SH AUTHOR
-This manual page was written by Carleos Artime <carleos at uniovi.es>,
-for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/loki/trunk/debian/rules
===================================================================
--- trunk/packages/loki/trunk/debian/rules 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/rules 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,115 +1,24 @@
#!/usr/bin/make -f
-# debian/rules for loki
-# Carleos Artime (carleos at uniovi.es)
-# GPL
+# debian/rules for loki using cdbs
+# Andreas Tille <tille at debian.org>, GPL
-# added after Andreas Tille's Makefile for fastlink:
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+
pkg=loki
-doc=$(pkg)-doc
+MANPAGES=check_het.1 \
+ hist.1 \
+ loki_count.1 \
+ loki_dist.1 \
+ loki_ext.1 \
+ loki_freq.1 \
+ loki_sort_error.1 \
+ prep.1 \
+ qavg.1
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-
-ifneq (,$(findstring debug,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -g
-endif
-ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
- INSTALL_PROGRAM += -s
-endif
-
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
- ./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
-
-
-build: build-stamp
-
-build-stamp: config.status
- dh_testdir
-
- # Add here commands to compile the package.
- $(MAKE)
- #/usr/bin/docbook-to-man debian/loki.sgml > loki.1
-
- touch build-stamp
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- # Add here commands to clean up after the build process.
- -$(MAKE) distclean
- -test -r /usr/share/misc/config.sub && \
- cp -f /usr/share/misc/config.sub config.sub
- -test -r /usr/share/misc/config.guess && \
- cp -f /usr/share/misc/config.guess config.guess
-
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- # Add here commands to install the package into debian/loki.
- $(MAKE) install prefix=$(CURDIR)/debian/loki/usr
-
- # Added after fastlink's makefile to split up into two packages:
-# mkdir -p `pwd`/debian/$(doc)/usr/share/doc/$(pkg)/docs
-# cp -a `pwd`/docs/*.ps `pwd`/debian/$(doc)/usr/share/doc/$(pkg)/docs
-# ln -s $(pkg) `pwd`/debian/$(doc)/usr/share/doc/$(doc)
-
-# Build architecture-independent files here.
-binary-indep: build install
- dh_testdir -i
- dh_testroot -i
-# dh_installdebconf
- dh_installdocs -i
- dh_installchangelogs -i
- dh_link -i
-# dh_strip
- dh_compress -i
- dh_fixperms -i
-# dh_makeshlibs
- dh_installdeb -i
-# dh_perl
-# dh_shlibdeps
- dh_gencontrol -i
- dh_md5sums -i
- dh_builddeb -i
-
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir -a
- dh_testroot -a
-# dh_installdebconf
- dh_installdocs -a
-# dh_installexamples
- dh_installmenu -a
- dh_installman -a debian/*.1
- dh_installchangelogs -a Changes
- dh_link -a
- dh_strip -a
- dh_compress -a
- dh_fixperms -a
-# dh_makeshlibs
- dh_installdeb -a
-# dh_perl
- dh_shlibdeps -a
- dh_gencontrol -a
- dh_md5sums -a
- dh_builddeb -a
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
+install/loki::
+ for man in $(MANPAGES) ; do \
+ ln -s loki.1.gz debian/$(pkg)/usr/share/man/man1/$${man}.gz ; \
+ done
+ make install prefix=$(CURDIR)/debian/loki/usr
Deleted: trunk/packages/loki/trunk/debian/watch
===================================================================
--- trunk/packages/loki/trunk/debian/watch 2008-03-21 05:51:38 UTC (rev 1642)
+++ trunk/packages/loki/trunk/debian/watch 2008-03-21 13:39:52 UTC (rev 1643)
@@ -1,6 +0,0 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# Site Directory Pattern Version Script
-version=2
-http://loki.homeunix.net/tar/loki_(.*)\.tar\.gz debian uupdate
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