[med-svn] [fasttree] branch upstream updated (520fc03 -> caef722)
This is an automated email from the git hooks/post-receive script. alteholz pushed a change to branch upstream in repository fasttree. from 520fc03 Imported Upstream version 2.1.9 new caef722 Import Upstream version 2.1.10 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: changelog | 11 +++ fasttree.c | 22 ++ 2 files changed, 29 insertions(+), 4 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] 01/01: pristine-tar data for fasttree_2.1.10.orig.tar.xz
This is an automated email from the git hooks/post-receive script. alteholz pushed a commit to branch pristine-tar in repository fasttree. commit 1bd77ab82e316ff99f9e390202ed6d52af68eb2b Author: Thorsten Alteholz <deb...@alteholz.de> Date: Sat Sep 9 19:11:35 2017 +0200 pristine-tar data for fasttree_2.1.10.orig.tar.xz --- fasttree_2.1.10.orig.tar.xz.delta | Bin 0 -> 770 bytes fasttree_2.1.10.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/fasttree_2.1.10.orig.tar.xz.delta b/fasttree_2.1.10.orig.tar.xz.delta new file mode 100644 index 000..90f3d47 Binary files /dev/null and b/fasttree_2.1.10.orig.tar.xz.delta differ diff --git a/fasttree_2.1.10.orig.tar.xz.id b/fasttree_2.1.10.orig.tar.xz.id new file mode 100644 index 000..4eca929 --- /dev/null +++ b/fasttree_2.1.10.orig.tar.xz.id @@ -0,0 +1 @@ +e2760921e9a22c4476daaebca01cf129e5f68eb2 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] branch pristine-tar updated (e605955 -> 1bd77ab)
This is an automated email from the git hooks/post-receive script. alteholz pushed a change to branch pristine-tar in repository fasttree. from e605955 pristine-tar data for fasttree_2.1.9.orig.tar.xz new 1bd77ab pristine-tar data for fasttree_2.1.10.orig.tar.xz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: fasttree_2.1.10.orig.tar.xz.delta | Bin 0 -> 770 bytes fasttree_2.1.10.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 fasttree_2.1.10.orig.tar.xz.delta create mode 100644 fasttree_2.1.10.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] annotated tag upstream/2.1.10 created (now 772ea82)
This is an automated email from the git hooks/post-receive script. alteholz pushed a change to annotated tag upstream/2.1.10 in repository fasttree. at 772ea82 (tag) tagging caef722af6dc73fb315ed4b5da086305f5c54799 (commit) replaces upstream/2.1.9 tagged by Thorsten Alteholz on Sat Sep 9 19:11:34 2017 +0200 - Log - Upstream version 2.1.10 Thorsten Alteholz (1): Import Upstream version 2.1.10 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] annotated tag debian/2.1.10-1 created (now 78cd99f)
This is an automated email from the git hooks/post-receive script. alteholz pushed a change to annotated tag debian/2.1.10-1 in repository fasttree. at 78cd99f (tag) tagging 780b1a6b75efc4947b0d4592780a1b7372e137e3 (commit) replaces debian/2.1.9-2 tagged by Thorsten Alteholz on Sat Sep 9 19:11:35 2017 +0200 - Log - Debian release 2.1.10-1 Thorsten Alteholz (2): Import Upstream version 2.1.10 Import Debian changes 2.1.10-1 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] 02/02: Import Debian changes 2.1.10-1
This is an automated email from the git hooks/post-receive script. alteholz pushed a commit to branch master in repository fasttree. commit 780b1a6b75efc4947b0d4592780a1b7372e137e3 Merge: 262f9d1 caef722 Author: Thorsten Alteholz <deb...@alteholz.de> Date: Sat Sep 9 19:00:00 2017 +0200 Import Debian changes 2.1.10-1 fasttree (2.1.10-1) unstable; urgency=medium * New upstream version changelog| 11 +++ debian/changelog | 6 ++ fasttree.c | 22 ++ 3 files changed, 35 insertions(+), 4 deletions(-) diff --cc debian/changelog index e51799e,000..f6d01b2 mode 100644,00..100644 --- a/debian/changelog +++ b/debian/changelog @@@ -1,87 -1,0 +1,93 @@@ ++fasttree (2.1.10-1) unstable; urgency=medium ++ ++ * New upstream version ++ ++ -- Thorsten Alteholz <deb...@alteholz.de> Sat, 09 Sep 2017 19:00:00 +0200 ++ +fasttree (2.1.9-2) unstable; urgency=medium + + * Team upload + + [ Nadiya Sitdykova ] + * Add simple autopkgtest test-suite + + [ Graham Inggs ] + * Switch to debhelper 10 + * Update debian/copyright + * Bump Standards-Version to 4.0.0, no further changes + + -- Graham Inggs <gin...@debian.org> Thu, 29 Jun 2017 13:46:37 +0200 + +fasttree (2.1.9-1) unstable; urgency=medium + + * New upstream version + * Use xz compression for source tarball + * cme fix dpkg-control + * Better hardening + + -- Andreas Tille <ti...@debian.org> Wed, 20 Apr 2016 22:17:07 +0200 + +fasttree (2.1.8-2) unstable; urgency=medium + + * Upload to unstable + + -- Andreas Tille <ti...@debian.org> Fri, 17 Jul 2015 21:02:15 +0200 + +fasttree (2.1.8-1) experimental; urgency=medium + + [ Andreas Tille ] + * Move debian/upstream to debian/upstream/metadata + * cme fix dpkg-control + * Priority: optional + * d/rules: cleanup from cruft + + [ Roland Fehrenbacher ] + * New upstream version 2.1.8 + * Makes debian/patches/increase-branch-length-precision.patch obsolete + + -- Roland Fehrenbacher <r...@q-leap.de> Tue, 31 Mar 2015 10:54:39 + + +fasttree (2.1.7-2) unstable; urgency=low + + * Team upload + * Modify/add patches to use double precision and increase branch +length precision. This is absolutely crucial to prevent flawed datas +analysis as described e.g. in +http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html +Closes: #781259 + + -- Roland Fehrenbacher <r...@q-leap.de> Tue, 24 Mar 2015 18:37:23 + + +fasttree (2.1.7-1biolinux1) precise; urgency=low + + * Added upstream changelog into package and backport for +Bio-Linux. + * Fixed clean: target to remove both binaries. + + -- Tim Booth <tbo...@ceh.ac.uk> Tue, 25 Feb 2014 12:50:42 + + +fasttree (2.1.7-1) unstable; urgency=low + + * New upstream version + * debian/control: remove DM-Upload-Allowed: + * debian/control: bump standards version to 3.9.4 + + -- Thorsten Alteholz <deb...@alteholz.de> Mon, 06 May 2013 18:00:00 +0200 + +fasttree (2.1.5-1) unstable; urgency=low + + * New upstream version + + -- Thorsten Alteholz <deb...@alteholz.de> Fri, 02 Nov 2012 18:00:00 +0100 + +fasttree (2.1.4-2) UNRELEASED; urgency=low + + * Fix name of upstream file and add eprint + + -- Andreas Tille <ti...@debian.org> Sat, 16 Jun 2012 09:42:29 +0200 + +fasttree (2.1.4-1) unstable; urgency=low + + * Initial release (Closes: #677648) + + -- Thorsten Alteholz <deb...@alteholz.de> Fri, 15 Jun 2012 19:52:56 +0200 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] branch master updated (262f9d1 -> 780b1a6)
This is an automated email from the git hooks/post-receive script. alteholz pushed a change to branch master in repository fasttree. from 262f9d1 Prepare for upload to unstable new caef722 Import Upstream version 2.1.10 new 780b1a6 Import Debian changes 2.1.10-1 The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: changelog| 11 +++ debian/changelog | 6 ++ fasttree.c | 22 ++ 3 files changed, 35 insertions(+), 4 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fasttree] 01/02: Import Upstream version 2.1.10
This is an automated email from the git hooks/post-receive script.
alteholz pushed a commit to branch master
in repository fasttree.
commit caef722af6dc73fb315ed4b5da086305f5c54799
Author: Thorsten Alteholz <deb...@alteholz.de>
Date: Sat Sep 9 19:11:34 2017 +0200
Import Upstream version 2.1.10
---
changelog | 11 +++
fasttree.c | 22 ++
2 files changed, 29 insertions(+), 4 deletions(-)
diff --git a/changelog b/changelog
index 3e34002..e49d015 100644
--- a/changelog
+++ b/changelog
@@ -1,3 +1,14 @@
+Version 2.1.10: April 11, 2017
+
+ Fix a bug when using GTR models with huge alignments with over 2
+ billion non-gap characters. The frequencies of A, C, G, and T were
+ being computed with a 32-bit (signed) counter. This led to
+ negative frequencies and eventually to a crash with
+ "FastTree.c:9769: tqli: Assertion `iter < 30' failed.". SetMLGtr()
+ now uses 64-bit counters. Also, more information about the
+ optimization of the GTR model is savd in the log file (if using
+ the -log option). To support this, gtr_opt_t now includes fpLog.
+
Version 2.1.9: March 29, 2016
Add the -lg option to use Le/Gascuel model for amino acid
diff --git a/fasttree.c b/fasttree.c
index 120477f..57c6fda 100644
--- a/fasttree.c
+++ b/fasttree.c
@@ -343,7 +343,7 @@ typedef float numeric_t;
#endif /* USE_SSE3 */
-#define FT_VERSION "2.1.9"
+#define FT_VERSION "2.1.10"
char *usage =
" FastTree protein_alignment > tree\n"
@@ -1380,6 +1380,7 @@ typedef struct {
double freq[4];
double rates[6];
int iRate; /* which rate to set x from */
+ FILE *fpLog; /* OPTIONAL WRITE */
} gtr_opt_t;
/* Returns -log_likelihood for the tree with the given rates
@@ -5848,11 +5849,14 @@ void SetMLGtr(/*IN/OUT*/NJ_t *NJ, /*OPTIONAL IN*/double
*freq_in, /*OPTIONAL WRI
assert(nCodes==4);
gtr_opt_t gtr;
gtr.NJ = NJ;
+ gtr.fpLog = fpLog;
if (freq_in != NULL) {
for (i=0; i<4; i++)
gtr.freq[i]=freq_in[i];
} else {
-int n[4] = {1,1,1,1}; /* pseudocounts */
+/* n[] and sum were int in FastTree 2.1.9 and earlier -- this
+ caused gtr analyses to fail on analyses with >2e9 positions */
+long n[4] = {1,1,1,1}; /* pseudocounts */
for (i=0; inSeq; i++) {
unsigned char *codes = NJ->profiles[i]->codes;
int iPos;
@@ -5860,7 +5864,7 @@ void SetMLGtr(/*IN/OUT*/NJ_t *NJ, /*OPTIONAL IN*/double
*freq_in, /*OPTIONAL WRI
if (codes[iPos] < 4)
n[codes[iPos]]++;
}
-int sum = n[0]+n[1]+n[2]+n[3];
+long sum = n[0]+n[1]+n[2]+n[3];
for (i=0; i<4; i++)
gtr.freq[i] = n[i]/(double)sum;
}
@@ -5903,6 +5907,7 @@ void SetMLGtr(/*IN/OUT*/NJ_t *NJ, /*OPTIONAL IN*/double
*freq_in, /*OPTIONAL WRI
}
double GTRNegLogLk(double x, void *data) {
+
gtr_opt_t *gtr = (gtr_opt_t*)data;
assert(nCodes == 4);
assert(gtr->NJ != NULL);
@@ -5915,6 +5920,12 @@ double GTRNegLogLk(double x, void *data) {
rates[i] = gtr->rates[i];
rates[gtr->iRate] = x;
+ FILE *fpLog = gtr->fpLog;
+ if (fpLog)
+fprintf(fpLog, "GTR_Opt\tfreq %.5f %.5f %.5f %.5f rates %.5f %.5f %.5f
%.5f %.5f %.5f\n",
+ gtr->freq[0], gtr->freq[1], gtr->freq[2], gtr->freq[3],
+ rates[0], rates[1], rates[2], rates[3], rates[4], rates[5]);
+
gtr->NJ->transmat = CreateGTR(rates, gtr->freq);
RecomputeMLProfiles(/*IN/OUT*/gtr->NJ);
double loglk = TreeLogLk(gtr->NJ, /*site_loglk*/NULL);
@@ -5923,7 +5934,10 @@ double GTRNegLogLk(double x, void *data) {
/* Do not recompute profiles -- assume the caller will do that */
if (verbose > 2)
fprintf(stderr, "GTR LogLk(%.5f %.5f %.5f %.5f %.5f %.5f) = %f\n",
- rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk);
+ rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk);
+ if (fpLog)
+fprintf(fpLog, "GTR_Opt\tGTR LogLk(%.5f %.5f %.5f %.5f %.5f %.5f) = %f\n",
+ rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk);
return(-loglk);
}
--
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[med-svn] r16815 - trunk/packages/mira/trunk/debian
Author: alteholz Date: 2014-04-26 18:02:31 + (Sat, 26 Apr 2014) New Revision: 16815 Modified: trunk/packages/mira/trunk/debian/changelog Log: new upstream version Modified: trunk/packages/mira/trunk/debian/changelog === --- trunk/packages/mira/trunk/debian/changelog 2014-04-25 22:17:49 UTC (rev 16814) +++ trunk/packages/mira/trunk/debian/changelog 2014-04-26 18:02:31 UTC (rev 16815) @@ -1,3 +1,9 @@ +mira (4.0.2-1) unstable; urgency=low + + * new upstream version + + -- Thorsten Alteholz deb...@alteholz.de Sat, 26 Apr 2014 19:00:35 +0200 + mira (4.0-1) unstable; urgency=low [ Thorsten Alteholz ] ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r16569 - in trunk/packages/vcftools/trunk/debian: . patches
Author: alteholz
Date: 2014-04-04 17:26:10 + (Fri, 04 Apr 2014)
New Revision: 16569
Modified:
trunk/packages/vcftools/trunk/debian/changelog
trunk/packages/vcftools/trunk/debian/control
trunk/packages/vcftools/trunk/debian/patches/make.patch
trunk/packages/vcftools/trunk/debian/rules
trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides
Log:
new upstream version
Modified: trunk/packages/vcftools/trunk/debian/changelog
===
--- trunk/packages/vcftools/trunk/debian/changelog 2014-04-04 16:33:47 UTC
(rev 16568)
+++ trunk/packages/vcftools/trunk/debian/changelog 2014-04-04 17:26:10 UTC
(rev 16569)
@@ -1,3 +1,10 @@
+vcftools (0.1.12+dfsg-1) unstable; urgency=low
+
+ * new upstream version
+ * debian/control: standard bumped to 3.9.5 (no changes)
+
+ -- Thorsten Alteholz deb...@alteholz.de Fri, 04 Apr 2014 18:00:00 +0200
+
vcftools (0.1.11+dfsg-1) unstable; urgency=low
* new upstream version
Modified: trunk/packages/vcftools/trunk/debian/control
===
--- trunk/packages/vcftools/trunk/debian/control2014-04-04 16:33:47 UTC
(rev 16568)
+++ trunk/packages/vcftools/trunk/debian/control2014-04-04 17:26:10 UTC
(rev 16569)
@@ -2,7 +2,7 @@
Section: science
Priority: extra
Build-Depends: debhelper (= 9), zlib1g-dev
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
Homepage: http://vcftools.sourceforge.net
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Uploaders: Thorsten Alteholz deb...@alteholz.de,
Modified: trunk/packages/vcftools/trunk/debian/patches/make.patch
===
--- trunk/packages/vcftools/trunk/debian/patches/make.patch 2014-04-04
16:33:47 UTC (rev 16568)
+++ trunk/packages/vcftools/trunk/debian/patches/make.patch 2014-04-04
17:26:10 UTC (rev 16569)
@@ -1,15 +1,18 @@
-Description: do not use MAKEFLAGS
+Description: do not use MAKEFLAGS and not MANDIR
Author: Thorsten Alteholz deb...@alteholz.de
-Last-Update: 2011-07-03
-Index: vcftools-0.1.7/Makefile
+Last-Update: 2014-04-03
+Index: vcftools_0.1.12/Makefile
===
vcftools_0.1.7.org/Makefile2011-07-04 15:22:33.0 +0200
-+++ vcftools_0.1.7/Makefile2011-07-04 15:22:56.0 +0200
-@@ -22,7 +22,7 @@
+--- vcftools_0.1.12.orig/Makefile 2014-04-04 10:37:59.0 +0200
vcftools_0.1.12/Makefile 2014-04-04 10:38:34.0 +0200
+@@ -25,9 +25,8 @@
+
DIRS = cpp perl
install:
- @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
+- @mkdir -p $(BINDIR); mkdir -p $(MODDIR); mkdir -p $(MANDIR); \
+- cp ${PREFIX}/cpp/vcftools.1.gz $(MANDIR); \
-for dir in $(DIRS); do cd $$dir $(MAKE) $(MAKEFLAGS) cd ..; done
++ @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
+for dir in $(DIRS); do cd $$dir $(MAKE) cd ..; done
clean:
Modified: trunk/packages/vcftools/trunk/debian/rules
===
--- trunk/packages/vcftools/trunk/debian/rules 2014-04-04 16:33:47 UTC (rev
16568)
+++ trunk/packages/vcftools/trunk/debian/rules 2014-04-04 17:26:10 UTC (rev
16569)
@@ -2,11 +2,16 @@
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
-# export DH_VERBOSE=1
+export DH_VERBOSE=1
%:
dh $@
+override_dh_auto_build:
+ echo hier bin ich
+ MAKEFLAGS= echo MAKEFLAGS is $(MAKEFLAGS)
+ MAKEFLAGS= make
+
override_dh_clean:
dh_clean
# [ -r Makefile ] make clean ?
Modified: trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides
===
--- trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides
2014-04-04 16:33:47 UTC (rev 16568)
+++ trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides
2014-04-04 17:26:10 UTC (rev 16569)
@@ -1,4 +1,5 @@
# the compiler flags are used
vcftools: hardening-no-fortify-functions usr/bin/vcftools
# this string does not appear in sources, it is just some binary blob
-vcftools: spelling-error-in-binary usr/bin/vcftools teH the
+# fixed upstream in 0.1.12
+#vcftools: spelling-error-in-binary usr/bin/vcftools teH the
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[med-svn] r16570 - trunk/packages/vcftools/trunk/debian
Author: alteholz Date: 2014-04-04 17:33:46 + (Fri, 04 Apr 2014) New Revision: 16570 Modified: trunk/packages/vcftools/trunk/debian/rules Log: do not use debug prints Modified: trunk/packages/vcftools/trunk/debian/rules === --- trunk/packages/vcftools/trunk/debian/rules 2014-04-04 17:26:10 UTC (rev 16569) +++ trunk/packages/vcftools/trunk/debian/rules 2014-04-04 17:33:46 UTC (rev 16570) @@ -7,11 +7,6 @@ %: dh $@ -override_dh_auto_build: - echo hier bin ich - MAKEFLAGS= echo MAKEFLAGS is $(MAKEFLAGS) - MAKEFLAGS= make - override_dh_clean: dh_clean # [ -r Makefile ] make clean ? ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r16410 - trunk/packages/parsinsert/trunk/debian
Author: alteholz Date: 2014-03-10 13:18:28 + (Mon, 10 Mar 2014) New Revision: 16410 Modified: trunk/packages/parsinsert/trunk/debian/copyright Log: it should be ...+ Modified: trunk/packages/parsinsert/trunk/debian/copyright === --- trunk/packages/parsinsert/trunk/debian/copyright2014-03-10 10:55:50 UTC (rev 16409) +++ trunk/packages/parsinsert/trunk/debian/copyright2014-03-10 13:18:28 UTC (rev 16410) @@ -5,9 +5,9 @@ Files: * Copyright: © 2007-2011 David Knox -License: GPL-3 +License: GPL-3+ -License: GPL-3 +License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or @@ -23,5 +23,5 @@ Files: debian/* Copyright: © 2014 Tim Booth tbo...@ceh.ac.uk -License: GPL-3 +License: GPL-3+ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15837 - trunk/packages/mgltools/pmv/trunk/debian/patches
Author: alteholz
Date: 2014-01-19 16:20:10 + (Sun, 19 Jan 2014)
New Revision: 15837
Added:
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
Log:
argh, it is still needed to maintain this version
Copied:
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
(from rev 14726,
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch)
===
---
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
(rev 0)
+++
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
2014-01-19 16:20:10 UTC (rev 15837)
@@ -0,0 +1,13 @@
+Index: Pmv-1.5.6~rc2+cvs.20111222/Pmv/stylesCommands.py
+===
+--- Pmv-1.5.6~rc2+cvs.20111222.orig/Pmv/stylesCommands.py 2011-10-01
01:36:21.0 +0200
Pmv-1.5.6~rc2+cvs.20111222/Pmv/stylesCommands.py 2011-12-23
21:57:47.0 +0100
+@@ -51,7 +51,7 @@
+ ## self.vf.undo.addEntry((undoCmd), (name))
+
+
+- def setupUndo(self, name):
++def setupUndo(self, name):
+ oldRendering = getRendering(self.vf.GUI.VIEWER)
+ self.undoRenderingStack.append(oldRendering)
+ self.vf.NEWundo.addUndoCall( ([(self.undo, (),{})], name))
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[med-svn] r15072 - trunk/packages/uc-echo/trunk/debian
Author: alteholz Date: 2013-10-30 21:41:47 + (Wed, 30 Oct 2013) New Revision: 15072 Added: trunk/packages/uc-echo/trunk/debian/README.Debian Modified: trunk/packages/uc-echo/trunk/debian/changelog trunk/packages/uc-echo/trunk/debian/rules Log: more architecture issues Added: trunk/packages/uc-echo/trunk/debian/README.Debian === --- trunk/packages/uc-echo/trunk/debian/README.Debian (rev 0) +++ trunk/packages/uc-echo/trunk/debian/README.Debian 2013-10-30 21:41:47 UTC (rev 15072) @@ -0,0 +1,7 @@ +According to upstream this program needs lots of RAM and thus for i386/amd64 +the compiler flag -m64 is needed. +Unfortunately this is not supported on all architectures. So on some (like +mips, mipsel, kfreebsd-i386, hurd-i386, armel, armhf), that have no 64-bit +mode implemented, only a 32bit version is built. +Apart from the number of data that can be processed, this has no influence +on the results. Modified: trunk/packages/uc-echo/trunk/debian/changelog === --- trunk/packages/uc-echo/trunk/debian/changelog 2013-10-30 15:22:10 UTC (rev 15071) +++ trunk/packages/uc-echo/trunk/debian/changelog 2013-10-30 21:41:47 UTC (rev 15072) @@ -1,3 +1,9 @@ +uc-echo (1.12-3) unstable; urgency=low + + * debian/rules: more architectures don't need -m64 + + -- Thorsten Alteholz deb...@alteholz.de Wed, 30 Oct 2013 19:00:07 +0100 + uc-echo (1.12-2) unstable; urgency=low * debian/control: use g++-multilib only when available (Closes: #727657) Modified: trunk/packages/uc-echo/trunk/debian/rules === --- trunk/packages/uc-echo/trunk/debian/rules 2013-10-30 15:22:10 UTC (rev 15071) +++ trunk/packages/uc-echo/trunk/debian/rules 2013-10-30 21:41:47 UTC (rev 15072) @@ -7,12 +7,10 @@ CPATH=/usr/include/$(gcc -print-multiarch) export LIBRARY_PATH CPATH ADDCXXFLAGS = -m64 -ifeq ($(DEB_HOST_ARCH),mips) +ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),mips mipsel kfreebsd-i386 hurd-i386 armel armhf ia64 )) ADDCXXFLAGS = endif -ifeq ($(DEB_HOST_ARCH),mipsel) -ADDCXXFLAGS = -endif + CXXFLAGS += $(ADDCXXFLAGS) %: ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15046 - in trunk/packages/uc-echo/trunk/debian: . patches
Author: alteholz Date: 2013-10-29 18:41:39 + (Tue, 29 Oct 2013) New Revision: 15046 Added: trunk/packages/uc-echo/trunk/debian/patches/m64-flag.patch Modified: trunk/packages/uc-echo/trunk/debian/changelog trunk/packages/uc-echo/trunk/debian/control trunk/packages/uc-echo/trunk/debian/patches/include.patch trunk/packages/uc-echo/trunk/debian/patches/series trunk/packages/uc-echo/trunk/debian/rules Log: make it compile on more archs Modified: trunk/packages/uc-echo/trunk/debian/changelog === --- trunk/packages/uc-echo/trunk/debian/changelog 2013-10-29 14:33:53 UTC (rev 15045) +++ trunk/packages/uc-echo/trunk/debian/changelog 2013-10-29 18:41:39 UTC (rev 15046) @@ -1,3 +1,10 @@ +uc-echo (1.12-2) unstable; urgency=low + + * debian/control: use g++-multilib only when available (Closes: #727657) + * add patch to compile on mips/mipsel + + -- Thorsten Alteholz deb...@alteholz.de Mon, 28 Oct 2013 19:00:07 +0100 + uc-echo (1.12-1) unstable; urgency=low * initial version (Closes: #704902) Modified: trunk/packages/uc-echo/trunk/debian/control === --- trunk/packages/uc-echo/trunk/debian/control 2013-10-29 14:33:53 UTC (rev 15045) +++ trunk/packages/uc-echo/trunk/debian/control 2013-10-29 18:41:39 UTC (rev 15046) @@ -7,7 +7,7 @@ python-all-dev (=2.6), python-scipy, python-numpy, - g++-multilib + g++-multilib [amd64 i386 kfreebsd-amd64 mips mipsel powerpc ppc64 s390x sparc sparc64 x32] Standards-Version: 3.9.4 Homepage: http://uc-echo.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/uc-echo/trunk/ Modified: trunk/packages/uc-echo/trunk/debian/patches/include.patch === --- trunk/packages/uc-echo/trunk/debian/patches/include.patch 2013-10-29 14:33:53 UTC (rev 15045) +++ trunk/packages/uc-echo/trunk/debian/patches/include.patch 2013-10-29 18:41:39 UTC (rev 15046) @@ -2,8 +2,8 @@ Description: add #include unistd.h for definition of open() Index: echo_v1_12/MMAP.hpp === echo_v1_12.orig/MMAP.hpp 2013-04-02 17:40:01.0 +0200 -+++ echo_v1_12/MMAP.hpp2013-04-02 17:40:01.0 +0200 +--- echo_v1_12.orig/MMAP.hpp 2013-10-28 11:44:22.0 +0100 echo_v1_12/MMAP.hpp2013-10-28 11:44:22.0 +0100 @@ -6,6 +6,7 @@ #include sys/stat.h #include fcntl.h Added: trunk/packages/uc-echo/trunk/debian/patches/m64-flag.patch === --- trunk/packages/uc-echo/trunk/debian/patches/m64-flag.patch (rev 0) +++ trunk/packages/uc-echo/trunk/debian/patches/m64-flag.patch 2013-10-29 18:41:39 UTC (rev 15046) @@ -0,0 +1,17 @@ +Author: Thorsten Alteholz deb...@alteholz.de +Description: don't use -m64 on all architectures +Index: echo_v1_12/Makefile +=== +--- echo_v1_12.orig/Makefile 2013-10-28 11:44:22.0 +0100 echo_v1_12/Makefile2013-10-28 11:45:58.0 +0100 +@@ -1,5 +1,9 @@ + CXX = g++ +-CXXFLAGS += -Wall -O3 -m64 $(CLFAGS) $(CPPFLAGS) ++# ++# the flag -m64 has been removed here ++# it will be applied by debian/ruls as it is not available ++# on certain architectures like mips ++CXXFLAGS += -Wall -O3 $(CLFAGS) $(CPPFLAGS) + HEADERS = *.hpp + LIB = DNASeq.o NeighborSet.o KmerHashMap.o + TARGETS = hashing NeighborJoin NeighborJoinParam NeighborMerge Voting HashMerge Modified: trunk/packages/uc-echo/trunk/debian/patches/series === --- trunk/packages/uc-echo/trunk/debian/patches/series 2013-10-29 14:33:53 UTC (rev 15045) +++ trunk/packages/uc-echo/trunk/debian/patches/series 2013-10-29 18:41:39 UTC (rev 15046) @@ -1,2 +1,3 @@ hardening-flags.patch include.patch +m64-flag.patch Modified: trunk/packages/uc-echo/trunk/debian/rules === --- trunk/packages/uc-echo/trunk/debian/rules 2013-10-29 14:33:53 UTC (rev 15045) +++ trunk/packages/uc-echo/trunk/debian/rules 2013-10-29 18:41:39 UTC (rev 15046) @@ -2,13 +2,28 @@ # DH_VERBOSE := 1 +DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH) LIBRARY_PATH=/usr/lib/$(gcc -print-multiarch) CPATH=/usr/include/$(gcc -print-multiarch) export LIBRARY_PATH CPATH +ADDCXXFLAGS = -m64 +ifeq ($(DEB_HOST_ARCH),mips) +ADDCXXFLAGS = +endif +ifeq ($(DEB_HOST_ARCH),mipsel) +ADDCXXFLAGS = +endif +CXXFLAGS += $(ADDCXXFLAGS) %: dh $@ --with python2 +override_dh_auto_build: + echo I: DEB_HOST_ARCH: $(DEB_HOST_ARCH) + echo I: ADDCXXFLAGS: $(ADDCXXFLAGS) + echo I: CXXFLAGS: $(CXXFLAGS) + dh_auto_build + override_dh_auto_install
[med-svn] r15047 - trunk/packages/uc-echo/trunk/debian
Author: alteholz Date: 2013-10-29 18:54:39 + (Tue, 29 Oct 2013) New Revision: 15047 Modified: trunk/packages/uc-echo/trunk/debian/changelog trunk/packages/uc-echo/trunk/debian/control trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides Log: use canonical vcs-fields Modified: trunk/packages/uc-echo/trunk/debian/changelog === --- trunk/packages/uc-echo/trunk/debian/changelog 2013-10-29 18:41:39 UTC (rev 15046) +++ trunk/packages/uc-echo/trunk/debian/changelog 2013-10-29 18:54:39 UTC (rev 15047) @@ -1,9 +1,10 @@ uc-echo (1.12-2) unstable; urgency=low * debian/control: use g++-multilib only when available (Closes: #727657) + * debian/control: use canonical vcs-fields * add patch to compile on mips/mipsel - -- Thorsten Alteholz deb...@alteholz.de Mon, 28 Oct 2013 19:00:07 +0100 + -- Thorsten Alteholz deb...@alteholz.de Tue, 29 Oct 2013 19:00:07 +0100 uc-echo (1.12-1) unstable; urgency=low Modified: trunk/packages/uc-echo/trunk/debian/control === --- trunk/packages/uc-echo/trunk/debian/control 2013-10-29 18:41:39 UTC (rev 15046) +++ trunk/packages/uc-echo/trunk/debian/control 2013-10-29 18:54:39 UTC (rev 15047) @@ -10,8 +10,8 @@ g++-multilib [amd64 i386 kfreebsd-amd64 mips mipsel powerpc ppc64 s390x sparc sparc64 x32] Standards-Version: 3.9.4 Homepage: http://uc-echo.sourceforge.net/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/uc-echo/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/uc-echo/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/uc-echo/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/uc-echo/trunk/ Package: uc-echo Architecture: any Modified: trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides === --- trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides 2013-10-29 18:41:39 UTC (rev 15046) +++ trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides 2013-10-29 18:54:39 UTC (rev 15047) @@ -1,8 +1,8 @@ # these flags are really used -uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/HashMerge -uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoin -uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoinParam uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborMerge uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/Voting -uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/hashing +#uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/HashMerge +#uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoin +#uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoinParam +#uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/hashing ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14916 - trunk/packages/staden-io-lib/trunk/debian
Author: alteholz Date: 2013-10-22 17:18:44 + (Tue, 22 Oct 2013) New Revision: 14916 Modified: trunk/packages/staden-io-lib/trunk/debian/changelog Log: update description Modified: trunk/packages/staden-io-lib/trunk/debian/changelog === --- trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-22 09:21:43 UTC (rev 14915) +++ trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-22 17:18:44 UTC (rev 14916) @@ -1,7 +1,7 @@ staden-io-lib (1.13.2-3) unstable; urgency=low * debian/patches: add patch to build on hurd_i386 - * no need to remove package from architecture anymore (Closes: #726875) + * no need to remove package from mips anymore (Closes: #726875) -- Thorsten Alteholz deb...@alteholz.de Mon, 21 Oct 2013 18:10:59 +0200 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14907 - in trunk/packages/staden-io-lib/trunk/debian: . patches
Author: alteholz
Date: 2013-10-21 19:58:48 + (Mon, 21 Oct 2013)
New Revision: 14907
Added:
trunk/packages/staden-io-lib/trunk/debian/patches/
trunk/packages/staden-io-lib/trunk/debian/patches/pathmax.patch
trunk/packages/staden-io-lib/trunk/debian/patches/series
Modified:
trunk/packages/staden-io-lib/trunk/debian/changelog
trunk/packages/staden-io-lib/trunk/debian/control
trunk/packages/staden-io-lib/trunk/debian/rules
Log:
make it available on hurd-i386, mips and sparc
Modified: trunk/packages/staden-io-lib/trunk/debian/changelog
===
--- trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-20 20:24:18 UTC
(rev 14906)
+++ trunk/packages/staden-io-lib/trunk/debian/changelog 2013-10-21 19:58:48 UTC
(rev 14907)
@@ -1,3 +1,11 @@
+staden-io-lib (1.13.2-3) unstable; urgency=low
+
+ * debian/rules: tests on sparc fail (no reason found yet)
+ * debian/patches: add patch to build on hurd_i386
+ * no need to remove package from architecture anymore (Closes: #726875)
+
+ -- Thorsten Alteholz deb...@alteholz.de Mon, 21 Oct 2013 18:10:59 +0200
+
staden-io-lib (1.13.2-2) unstable; urgency=low
* Restore and update symbols file debian/libstaden-read1.symbols.
Modified: trunk/packages/staden-io-lib/trunk/debian/control
===
--- trunk/packages/staden-io-lib/trunk/debian/control 2013-10-20 20:24:18 UTC
(rev 14906)
+++ trunk/packages/staden-io-lib/trunk/debian/control 2013-10-21 19:58:48 UTC
(rev 14907)
@@ -1,7 +1,8 @@
Source: staden-io-lib
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Uploaders: Charles Plessy ple...@debian.org,
- Andreas Tille ti...@debian.org
+ Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
Section: science
Priority: optional
Build-Depends: debhelper (= 9),
Added: trunk/packages/staden-io-lib/trunk/debian/patches/pathmax.patch
===
--- trunk/packages/staden-io-lib/trunk/debian/patches/pathmax.patch
(rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/pathmax.patch
2013-10-21 19:58:48 UTC (rev 14907)
@@ -0,0 +1,98 @@
+Author: Thorsten Alteholz deb...@alteholz.de
+Description: define PATH_MAX in case it is not available
+ this is needed to compile on hurd_i386
+Index: staden-io-lib-1.13.2/io_lib/cram_index.c
+===
+--- staden-io-lib-1.13.2.orig/io_lib/cram_index.c 2013-10-21
20:01:06.0 +0200
staden-io-lib-1.13.2/io_lib/cram_index.c 2013-10-21 20:01:05.0
+0200
+@@ -43,6 +43,14 @@
+ #include io_lib/os.h
+ #include io_lib/zfio.h
+
++/*
++ define PATH_MAX in case it is not available
++ (for example for hurd_i386)
++*/
++#ifndef PATH_MAX
++#define PATH_MAX 4096
++#endif
++
+ #if 0
+ static void dump_index_(cram_index *e, int level) {
+ int i, n;
+Index: staden-io-lib-1.13.2/io_lib/cram_io.c
+===
+--- staden-io-lib-1.13.2.orig/io_lib/cram_io.c 2013-10-21 20:01:06.0
+0200
staden-io-lib-1.13.2/io_lib/cram_io.c 2013-10-21 20:01:05.0
+0200
+@@ -39,6 +39,14 @@
+ #include io_lib/md5.h
+ #include io_lib/open_trace_file.h
+
++/*
++ define PATH_MAX in case it is not available
++ (for example for hurd_i386)
++*/
++#ifndef PATH_MAX
++#define PATH_MAX 4096
++#endif
++
+ //#define REF_DEBUG
+
+ #ifdef REF_DEBUG
+Index: staden-io-lib-1.13.2/io_lib/files.c
+===
+--- staden-io-lib-1.13.2.orig/io_lib/files.c 2013-10-21 20:01:06.0
+0200
staden-io-lib-1.13.2/io_lib/files.c2013-10-21 20:01:05.0
+0200
+@@ -18,6 +18,14 @@
+
+ #include io_lib/misc.h
+
++/*
++ define PATH_MAX in case it is not available
++ (for example for hurd_i386)
++*/
++#ifndef PATH_MAX
++#define PATH_MAX 4096
++#endif
++
+ #include sys/types.h
+ #include sys/stat.h
+ /* Alliant's Concentrix sys/stat.h is hugely deficient */
+Index: staden-io-lib-1.13.2/io_lib/srf.h
+===
+--- staden-io-lib-1.13.2.orig/io_lib/srf.h 2013-10-21 20:01:06.0
+0200
staden-io-lib-1.13.2/io_lib/srf.h 2013-10-21 20:01:58.0 +0200
+@@ -5,6 +5,14 @@
+ #include io_lib/ztr.h
+ #include io_lib/mFILE.h
+
++/*
++ define PATH_MAX in case it is not available
++ (for example for hurd_i386)
++*/
++#ifndef PATH_MAX
++#define PATH_MAX 4096
++#endif
++
+ #define SRF_MAGIC SSRF
+ #define SRF_VERSION 1.3
+
+Index: staden-io-lib-1.13.2/progs/cram_index.c
+===
+--- staden-io-lib-1.13.2.orig/progs/cram_index.c 2013-10-21
20:01:06.0
[med-svn] r14763 - in trunk/packages/cluster3/trunk/debian: . patches
Author: alteholz
Date: 2013-09-26 17:48:41 + (Thu, 26 Sep 2013)
New Revision: 14763
Added:
trunk/packages/cluster3/trunk/debian/patches/build-on-arm.patch
Modified:
trunk/packages/cluster3/trunk/debian/changelog
trunk/packages/cluster3/trunk/debian/patches/series
Log:
build on arm patch
Modified: trunk/packages/cluster3/trunk/debian/changelog
===
--- trunk/packages/cluster3/trunk/debian/changelog 2013-09-26 10:55:29 UTC
(rev 14762)
+++ trunk/packages/cluster3/trunk/debian/changelog 2013-09-26 17:48:41 UTC
(rev 14763)
@@ -1,3 +1,9 @@
+cluster3 (1.52-2) unstable; urgency=low
+
+ * add patch from Stefano Rivera (build on armhf) (Closes: #723561)
+
+ -- Thorsten Alteholz deb...@alteholz.de Thu, 26 Sep 2013 18:00:00 +0200
+
cluster3 (1.52-1) unstable; urgency=low
* rebuild needed for motif transition (Closes: #713062)
Added: trunk/packages/cluster3/trunk/debian/patches/build-on-arm.patch
===
--- trunk/packages/cluster3/trunk/debian/patches/build-on-arm.patch
(rev 0)
+++ trunk/packages/cluster3/trunk/debian/patches/build-on-arm.patch
2013-09-26 17:48:41 UTC (rev 14763)
@@ -0,0 +1,18 @@
+Author: Stefano Rivera stefa...@debian.org
+Description: let pacakage build on armhf
+--- a/src/Makefile.PL
b/src/Makefile.PL
+@@ -2,10 +2,10 @@
+ use Config;
+ use POSIX;
+
+-# Check if this is a 64 bit machine
++# Check if this is an arch where we need position independent code
+ my $CCFLAGS = '';
+ my $machine = (POSIX::uname())[4];
+-if ($machine =~ /64/) {
++if ($machine =~ /64|arm/) {
+ $CCFLAGS = '-fPIC';
+ }
+
+
Modified: trunk/packages/cluster3/trunk/debian/patches/series
===
--- trunk/packages/cluster3/trunk/debian/patches/series 2013-09-26 10:55:29 UTC
(rev 14762)
+++ trunk/packages/cluster3/trunk/debian/patches/series 2013-09-26 17:48:41 UTC
(rev 14763)
@@ -1 +1,2 @@
#compile-warnings.patch
+build-on-arm.patch
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[med-svn] r14731 - in trunk/packages/treeview/trunk/debian: . patches
Author: alteholz
Date: 2013-09-17 17:46:06 + (Tue, 17 Sep 2013)
New Revision: 14731
Modified:
trunk/packages/treeview/trunk/debian/changelog
trunk/packages/treeview/trunk/debian/patches/classpath.patch
Log:
new release
Modified: trunk/packages/treeview/trunk/debian/changelog
===
--- trunk/packages/treeview/trunk/debian/changelog 2013-09-17 17:32:22 UTC
(rev 14730)
+++ trunk/packages/treeview/trunk/debian/changelog 2013-09-17 17:46:06 UTC
(rev 14731)
@@ -1,3 +1,9 @@
+treeview (1.1.6.4+dfsg-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 17 Sep 2013 18:00:00 +0200
+
treeview (1.1.6.3+dfsg-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/treeview/trunk/debian/patches/classpath.patch
===
--- trunk/packages/treeview/trunk/debian/patches/classpath.patch
2013-09-17 17:32:22 UTC (rev 14730)
+++ trunk/packages/treeview/trunk/debian/patches/classpath.patch
2013-09-17 17:46:06 UTC (rev 14731)
@@ -1,9 +1,9 @@
Description: do not use internal lib
Author: Thorsten Alteholz deb...@alteholz.de
-Index: treeview_1.1.6.2+dfsg.orig/build.xml
+Index: treeview_1.1.6.4+dfsg.orig/build.xml
===
treeview_1.1.6.2+dfsg.orig.orig/build.xml 2013-04-26 10:24:51.0
+0200
-+++ treeview_1.1.6.2+dfsg.orig/build.xml 2013-04-26 10:45:16.0
+0200
+--- treeview_1.1.6.4+dfsg.orig.orig/build.xml 2013-09-17 12:56:26.0
+0200
treeview_1.1.6.4+dfsg.orig/build.xml 2013-09-17 12:59:03.0
+0200
@@ -83,6 +83,9 @@
fileset dir=${app.libs}
include name=*.jar/
@@ -41,29 +41,56 @@
/copy
move file =${plugin.dir} todir=applet
/move
-@@ -342,6 +345,7 @@
+@@ -337,51 +340,11 @@
+ delete file=${app.jar} /
+ delete dir=${dist.home} /
+ delete dir=applet /
+- delete dir=bundle /
+ /target
!-- some stuff for Mac OSX application bundles... --
!-- unfortunately, this only work on max os X right now. --
-+!-- This is just needed for os X, so no need for Debian
- taskdef name=jarbundler
-classname=net.sourceforge.jarbundler.JarBundler
- classpath
-@@ -359,7 +363,7 @@
- jarbundler dir=bundle/TreeView
- name=Java TreeView
-
mainclass=edu.stanford.genetics.treeview.app.LinkedViewApp
+-taskdef name=jarbundler
+- classname=net.sourceforge.jarbundler.JarBundler
+- classpath
+- pathelement path=${compile.lib}/jarbundler-1.8.1.jar /
+- pathelement path=${compile.lib}/xercesImpl.jar /
+- pathelement path=${compile.lib}/xml-apis.jar /
+- /classpath
+-/taskdef
+-
+-target name=bundle depends=jar,plugins
+- description=Make a mac application bundle
+-delete dir=bundle /
+- mkdir dir=bundle/
+- mkdir dir=bundle/TreeView/
+- jarbundler dir=bundle/TreeView
+-name=Java TreeView
+-
mainclass=edu.stanford.genetics.treeview.app.LinkedViewApp
-jars=TreeView.jar lib/nanoxml-2.2.2.jar
-+jars=TreeView.jar /usr/share/java/nanoxml.jar
-
icon=static/images/treeviewIcon.icns
-
version=1.1.6r2
-
aboutmenuname=Java TreeView
-@@ -381,7 +385,7 @@
- delete file=TreeView.jar/
-
- /target
+-
icon=static/images/treeviewIcon.icns
+-
version=1.1.6r4
+-
aboutmenuname=Java TreeView
+-
vmoptions=-Xmx500m -Dapple.awt.TextAntialiasing=false
+-
arguments=-b .
+-
/
+- mkdir dir=bundle/TreeView/images/
+- copy todir=bundle/TreeView/images
+- fileset dir=static/images/
+- /copy
+-move file =${plugin.dir} todir=bundle/TreeView
+-/move
-
-+--
+- mkdir dir=bundle/TreeView/coordinates/
+- copy todir=bundle/TreeView/coordinates
+- fileset dir=static/coordinates/
+- /copy
+-
+- delete file=TreeView.jar/
+-
+-/target
+-
++!-- not needed for Debian so remove this --
___
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[med-svn] r14724 - in trunk/packages/cluster3/trunk/debian: . patches
Author: alteholz Date: 2013-09-16 17:21:28 + (Mon, 16 Sep 2013) New Revision: 14724 Modified: trunk/packages/cluster3/trunk/debian/changelog trunk/packages/cluster3/trunk/debian/control trunk/packages/cluster3/trunk/debian/patches/series trunk/packages/cluster3/trunk/debian/rules trunk/packages/cluster3/trunk/debian/xcluster3.sgml Log: new upstream version Modified: trunk/packages/cluster3/trunk/debian/changelog === --- trunk/packages/cluster3/trunk/debian/changelog 2013-09-16 14:48:13 UTC (rev 14723) +++ trunk/packages/cluster3/trunk/debian/changelog 2013-09-16 17:21:28 UTC (rev 14724) @@ -1,3 +1,13 @@ +cluster3 (1.52-1) unstable; urgency=low + + * rebuild needed for motif transition (Closes: #713062) + * New upstream release (1.52) + * debian/xcluster3.sgml: fix errors + * debian/control: canonical vcs-* fields + * debin/control: bumped to 3.9.4 (no changes) + + -- Thorsten Alteholz deb...@alteholz.de Mon, 16 Sep 2013 19:00:00 +0200 + cluster3 (1.50-1) unstable; urgency=low [ Thorsten Alteholz ] Modified: trunk/packages/cluster3/trunk/debian/control === --- trunk/packages/cluster3/trunk/debian/control2013-09-16 14:48:13 UTC (rev 14723) +++ trunk/packages/cluster3/trunk/debian/control2013-09-16 17:21:28 UTC (rev 14724) @@ -15,10 +15,10 @@ libsm-dev, libxt-dev, docbook-to-man -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cluster3/trunk/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cluster3/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cluster3/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cluster3/trunk/ Package: cluster3 Architecture: any Modified: trunk/packages/cluster3/trunk/debian/patches/series === --- trunk/packages/cluster3/trunk/debian/patches/series 2013-09-16 14:48:13 UTC (rev 14723) +++ trunk/packages/cluster3/trunk/debian/patches/series 2013-09-16 17:21:28 UTC (rev 14724) @@ -1 +1 @@ -compile-warnings.patch +#compile-warnings.patch Modified: trunk/packages/cluster3/trunk/debian/rules === --- trunk/packages/cluster3/trunk/debian/rules 2013-09-16 14:48:13 UTC (rev 14723) +++ trunk/packages/cluster3/trunk/debian/rules 2013-09-16 17:21:28 UTC (rev 14724) @@ -62,7 +62,8 @@ install-arch-perl: install-arch-perl-stamp install-arch-perl-stamp: - perl Makefile.PL prefix=$(CURDIR)/debian/cluster3/usr/ + #error with prefix defined: perl Makefile.PL prefix=$(CURDIR)/debian/cluster3/usr/ + perl Makefile.PL make make test make install Modified: trunk/packages/cluster3/trunk/debian/xcluster3.sgml === --- trunk/packages/cluster3/trunk/debian/xcluster3.sgml 2013-09-16 14:48:13 UTC (rev 14723) +++ trunk/packages/cluster3/trunk/debian/xcluster3.sgml 2013-09-16 17:21:28 UTC (rev 14724) @@ -62,6 +62,7 @@ refsynopsisdiv cmdsynopsis commandxdhpackage;/command +/cmdsynopsis /refsynopsisdiv refsect1 titleDESCRIPTION/title ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14725 - trunk/packages/cluster3/trunk/debian
Author: alteholz Date: 2013-09-16 17:48:11 + (Mon, 16 Sep 2013) New Revision: 14725 Modified: trunk/packages/cluster3/trunk/debian/rules Log: better this way Modified: trunk/packages/cluster3/trunk/debian/rules === --- trunk/packages/cluster3/trunk/debian/rules 2013-09-16 17:21:28 UTC (rev 14724) +++ trunk/packages/cluster3/trunk/debian/rules 2013-09-16 17:48:11 UTC (rev 14725) @@ -63,7 +63,7 @@ install-arch-perl: install-arch-perl-stamp install-arch-perl-stamp: #error with prefix defined: perl Makefile.PL prefix=$(CURDIR)/debian/cluster3/usr/ - perl Makefile.PL + perl Makefile.PL INSTALL_BASE=$(CURDIR)/debian/cluster3/usr/ make make test make install ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14677 - trunk/packages/dssp/trunk/debian
Author: alteholz Date: 2013-09-12 17:42:43 + (Thu, 12 Sep 2013) New Revision: 14677 Modified: trunk/packages/dssp/trunk/debian/control Log: use canonical vcs Modified: trunk/packages/dssp/trunk/debian/control === --- trunk/packages/dssp/trunk/debian/control2013-09-12 16:55:53 UTC (rev 14676) +++ trunk/packages/dssp/trunk/debian/control2013-09-12 17:42:43 UTC (rev 14677) @@ -12,8 +12,8 @@ libboost-thread-dev (= 1.42.0) Standards-Version: 3.9.4 Section: science -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dssp/trunk/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dssp/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/dssp/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dssp/trunk/ Homepage: http://www.cmbi.ru.nl/dssp.html Package: dssp ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14326 - trunk/packages/mgltools/sff/trunk/debian
Author: alteholz Date: 2013-08-03 15:07:17 + (Sat, 03 Aug 2013) New Revision: 14326 Modified: trunk/packages/mgltools/sff/trunk/debian/changelog Log: new upload for mgltools-sff Modified: trunk/packages/mgltools/sff/trunk/debian/changelog === --- trunk/packages/mgltools/sff/trunk/debian/changelog 2013-08-02 13:05:08 UTC (rev 14325) +++ trunk/packages/mgltools/sff/trunk/debian/changelog 2013-08-03 15:07:17 UTC (rev 14326) @@ -1,3 +1,9 @@ +mgltools-sff (1.5.7~rc1~cvs.20130519-2) unstable; urgency=low + + * new upload with different debian version (due to missing bhtree) + + -- Thorsten Alteholz deb...@alteholz.de Sat, 03 Aug 2013 16:00:00 +0200 + mgltools-sff (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14171 - trunk/packages/python-sqlsoup/trunk/debian
Author: alteholz Date: 2013-07-16 17:08:00 + (Tue, 16 Jul 2013) New Revision: 14171 Modified: trunk/packages/python-sqlsoup/trunk/debian/changelog trunk/packages/python-sqlsoup/trunk/debian/copyright Log: update copyright Modified: trunk/packages/python-sqlsoup/trunk/debian/changelog === --- trunk/packages/python-sqlsoup/trunk/debian/changelog2013-07-16 07:25:07 UTC (rev 14170) +++ trunk/packages/python-sqlsoup/trunk/debian/changelog2013-07-16 17:08:00 UTC (rev 14171) @@ -1,5 +1,6 @@ python-sqlsoup (0.9.0-1) unstable; urgency=low * initial release (Closes: #712411) + * debian/copyright: add missing entries - -- Thorsten Alteholz deb...@alteholz.de Sat, 15 Jun 2013 19:00:00 +0200 + -- Thorsten Alteholz deb...@alteholz.de Tue, 16 Jul 2013 18:00:00 +0200 Modified: trunk/packages/python-sqlsoup/trunk/debian/copyright === --- trunk/packages/python-sqlsoup/trunk/debian/copyright2013-07-16 07:25:07 UTC (rev 14170) +++ trunk/packages/python-sqlsoup/trunk/debian/copyright2013-07-16 17:08:00 UTC (rev 14171) @@ -6,6 +6,26 @@ Copyright: 2005-2012 by Jonathan Ellis and Michael Bayer. License: MIT +Files: docs/_static/jquery.js: +Copyright: 2010, John Resig + 2010, The Dojo Foundation +License: MIT + +Files: docs/_static/basic.css + docs/_static/doctools.js + docs/_static/nature.css: + docs/_static/searchtools.js: + docs/_static/websupport.js: +Copyright: 2007-2011 by the Sphinx team +License: BSD + +Files: docs/_static/underscore.js +Copyright: 2009 Jeremy Ashkenas, DocumentCloud Inc. +License: MIT + Underscore is freely distributable under the terms of the MIT license. + Portions of Underscore are inspired by or borrowed from Prototype.js, + Oliver Steele's Functional, and John Resig's Micro-Templating. + Files: debian/* Copyright: 2013 Thorsten Alteholz deb...@alteholz.de License: MIT @@ -30,3 +50,29 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +License: BSD + (According to website at http://sphinx-doc.org/ and package sphinx-common) + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + . + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14159 - trunk/packages/epigrass/tags
Author: alteholz Date: 2013-07-14 15:45:49 + (Sun, 14 Jul 2013) New Revision: 14159 Added: trunk/packages/epigrass/tags/2.2.2-1/ Log: add tag for 2.2.2-1 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14160 - in trunk/packages/epigrass: . branches branches/2.2.2-1 branches/2.2.2-1/debian
Author: alteholz Date: 2013-07-14 15:46:54 + (Sun, 14 Jul 2013) New Revision: 14160 Added: trunk/packages/epigrass/branches/ trunk/packages/epigrass/branches/2.2.2-1/ trunk/packages/epigrass/branches/2.2.2-1/debian/ Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog Log: add 2.2.2-1-branch and close #715433 Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog === --- trunk/packages/epigrass/trunk/debian/changelog 2013-05-16 15:15:39 UTC (rev 13605) +++ trunk/packages/epigrass/branches/2.2.2-1/debian/changelog 2013-07-14 15:46:54 UTC (rev 14160) @@ -1,3 +1,9 @@ +epigrass (2.2.2-2) unstable; urgency=low + + * rebuild package and remove dependency on python-sqlalchemy0.8 (Closes: #715433) + + -- Thorsten Alteholz deb...@alteholz.de Sun, 14 Jul 2013 17:00:00 +0200 + epigrass (2.2.2-1) unstable; urgency=low * new upstream version ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r14161 - trunk/packages/epigrass/branches/2.2.2-1/debian
Author: alteholz Date: 2013-07-14 16:00:51 + (Sun, 14 Jul 2013) New Revision: 14161 Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog Log: line too long Modified: trunk/packages/epigrass/branches/2.2.2-1/debian/changelog === --- trunk/packages/epigrass/branches/2.2.2-1/debian/changelog 2013-07-14 15:46:54 UTC (rev 14160) +++ trunk/packages/epigrass/branches/2.2.2-1/debian/changelog 2013-07-14 16:00:51 UTC (rev 14161) @@ -1,6 +1,6 @@ epigrass (2.2.2-2) unstable; urgency=low - * rebuild package and remove dependency on python-sqlalchemy0.8 (Closes: #715433) + * rebuild and remove dependency on python-sqlalchemy0.8 (Closes: #715433) -- Thorsten Alteholz deb...@alteholz.de Sun, 14 Jul 2013 17:00:00 +0200 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13886 - trunk/packages/mgltools/cadd/trunk/debian
Author: alteholz Date: 2013-06-08 17:25:18 + (Sat, 08 Jun 2013) New Revision: 13886 Modified: trunk/packages/mgltools/cadd/trunk/debian/changelog trunk/packages/mgltools/cadd/trunk/debian/rules Log: obsolete file prevents compiling Modified: trunk/packages/mgltools/cadd/trunk/debian/changelog === --- trunk/packages/mgltools/cadd/trunk/debian/changelog 2013-06-08 14:20:12 UTC (rev 13885) +++ trunk/packages/mgltools/cadd/trunk/debian/changelog 2013-06-08 17:25:18 UTC (rev 13886) @@ -1,3 +1,10 @@ +mgltools-cadd (1.5.7~rc1~cvs.20130519-2) unstable; urgency=low + + * debian/rules: remove obsolete file with syntax errors + (Closes: #711455) + + -- Thorsten Alteholz deb...@alteholz.de Sat, 08 Jun 2013 17:00:00 +0200 + mgltools-cadd (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. Modified: trunk/packages/mgltools/cadd/trunk/debian/rules === --- trunk/packages/mgltools/cadd/trunk/debian/rules 2013-06-08 14:20:12 UTC (rev 13885) +++ trunk/packages/mgltools/cadd/trunk/debian/rules 2013-06-08 17:25:18 UTC (rev 13886) @@ -14,6 +14,9 @@ override_dh_install: dh_install + # remove some obsolete file, change if file vanishes upstream + rm $(CURDIR)/debian/mgltools-cadd/usr/lib/python2.7/dist-packages/CADD/Raccoon2/RaccoonTools.py + find $(CURDIR)/debian/mgltools-cadd -name runCADD | xargs -r chmod 755 find $(CURDIR)/debian/mgltools-cadd -name *.prm -o -name *.res | xargs -r chmod -x find $(CURDIR)/debian/mgltools-cadd -name raccoonLauncher | xargs -r chmod -x ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13855 - in trunk/packages/mira/trunk/debian: . patches
)
-
- mostlyclean-compile:
- -rm -f *.$(OBJEXT)
Modified: trunk/packages/mira/trunk/debian/patches/series
===
--- trunk/packages/mira/trunk/debian/patches/series 2013-06-06 15:33:16 UTC
(rev 13854)
+++ trunk/packages/mira/trunk/debian/patches/series 2013-06-06 18:08:34 UTC
(rev 13855)
@@ -1,4 +1,5 @@
xsltproc_nonet_for_doc_build
-hardening-flags.patch
add_shebang_lines
boost1.53
+spelling.patch
+
Added: trunk/packages/mira/trunk/debian/patches/spelling.patch
===
--- trunk/packages/mira/trunk/debian/patches/spelling.patch
(rev 0)
+++ trunk/packages/mira/trunk/debian/patches/spelling.patch 2013-06-06
18:08:34 UTC (rev 13855)
@@ -0,0 +1,67 @@
+Author: Thorsten Alteholz deb...@alteholz.de
+Description: lintian complains about some spelling errors
+Index: mira-3.9.17/src/mira/assembly.C
+===
+--- mira-3.9.17.orig/src/mira/assembly.C 2013-05-21 20:10:33.0
+0200
mira-3.9.17/src/mira/assembly.C2013-06-06 11:20:57.0 +0200
+@@ -555,7 +555,7 @@
+ cerr \n\nOUCH! something strange ... tried more than 100 deletes of
basename ... list size is AS_usedtmpfiles.size() '\n';
+ }
+ if(numdeleted1200) {
+- cerr \n\nOUCH! something wierd ... tried more than 1200 deletes of
basename ... list size is AS_usedtmpfiles.size() '\n';
++ cerr \n\nOUCH! something weird ... tried more than 1200 deletes of
basename ... list size is AS_usedtmpfiles.size() '\n';
+ cerr We'll stop that here.\n;
+ return numdeleted;
+ }
+Index: mira-3.9.17/src/mira/maf_parse.C
+===
+--- mira-3.9.17.orig/src/mira/maf_parse.C 2013-05-21 20:10:33.0
+0200
mira-3.9.17/src/mira/maf_parse.C 2013-06-06 11:26:01.0 +0200
+@@ -985,7 +985,7 @@
+ MAF_read_seqtype=ReadGroupLib::stringToSeqType(actline);
+
+ if(MAF_read_seqtype==ReadGroupLib::SEQTYPE_END){
+-MIRANOTIFY(Notify::FATAL, Error in MAF_read_name in tag
acttoken : unkown sequencing type ' actline '?);
++MIRANOTIFY(Notify::FATAL, Error in MAF_read_name in tag
acttoken : unknown sequencing type ' actline '?);
+ }
+ FUNCEND();
+ }
+Index: mira-3.9.17/src/progs/mira.C
+===
+--- mira-3.9.17.orig/src/progs/mira.C 2013-05-21 20:10:33.0 +0200
mira-3.9.17/src/progs/mira.C 2013-06-06 11:20:16.0 +0200
+@@ -558,7 +558,7 @@
+ cout \nOptions:\n;
+ cout
+ -c / --cwd=\t\tdirectory\tChange working directory\n
+--r / --resume\t\t\t\tResume an interupted assembly\n
++-r / --resume\t\t\t\tResume an interrupted assembly\n
+ -h / --help\t\t\t\tPrint short help and exit\n
+ -v / --version\t\t\tPrint version and exit\n
+ ;
+Index: mira-3.9.17/src/io/gap4_ft_so_map.xxd
+===
+--- mira-3.9.17.orig/src/io/gap4_ft_so_map.xxd 2013-05-21 20:10:33.0
+0200
mira-3.9.17/src/io/gap4_ft_so_map.xxd 2013-06-06 11:34:24.0
+0200
+@@ -46,7 +46,7 @@
+ Fm-R misc_RNAtranscript SO:673 any transcript or RNA
product that cannot be defined by other RNA keys (prim_transcript,
precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS, sig_peptide,
transit_peptide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and
snRNA);An RNA synthesized on a DNA or RNA template by an RNA polymerase.
+ Fm-b misc_bindingbinding_siteSO:409 site in nucleic acid
which covalently or non-covalently binds another moiety that cannot be
described by any other binding key (primer_bind or protein_bind); A region on
the surface of a molecule that may interact with another molecule.
+ Fm-d misc_difference sequence_difference SO:413 feature
sequence is different from that presented in the entry and cannot be described
by any other Difference key (conflict, unsure, old_sequence, variation, or
modified_base);A region where the sequences differs from that of a
specified sequence.
+-Fm-f misc_featureregion SO:001 region of biological interest
which cannot be described by any other feature key; a new or rare feature;
Continous sequence.
++Fm-f misc_featureregion SO:001 region of biological interest
which cannot be described by any other feature key; a new or rare feature;
Continuous sequence.
+ Fm-r misc_recomb recombination_feature SO:298 site of any
generalized, site-specific or replicative recombination event where there is a
breakage and reunion of duplex DNA that cannot be described by other
recombination keys or qualifiers of source
[med-svn] r13848 - in trunk/packages/mira/trunk/debian: . patches
Author: alteholz Date: 2013-06-05 18:10:33 + (Wed, 05 Jun 2013) New Revision: 13848 Added: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install trunk/packages/mira/trunk/debian/patches/hardening-flags.patch Removed: trunk/packages/mira/trunk/debian/mira-assembler.install Modified: trunk/packages/mira/trunk/debian/changelog trunk/packages/mira/trunk/debian/compat trunk/packages/mira/trunk/debian/control trunk/packages/mira/trunk/debian/patches/series trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build trunk/packages/mira/trunk/debian/rules trunk/packages/mira/trunk/debian/watch Log: some progress Modified: trunk/packages/mira/trunk/debian/changelog === --- trunk/packages/mira/trunk/debian/changelog 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/changelog 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,3 +1,23 @@ +mira (3.9.17-1) UNRELEASED; urgency=low + + * new upstream version + * debian/control: Standards-Version set to 3.9.4 (no changes) + * debian/control: DM-Upload-Allowed: removed + * debian/control: use dh 9 + * debian/control: add dependency to libboost-iostreams-dev + * debian/rules: get-orig-source added + * debian/watch: do not look at dev-versions + * TODO: RC bug (gcc4.8) + boost 1.53 + lintian stuff: manpages +spelling errors +hardening flags for fastatool +extended description +docbase +Up to now the new version builds with old gcc and old boost. + + -- Thorsten Alteholz deb...@alteholz.de Wed, 05 Jun 2013 18:00:01 +0200 + mira (3.4.0.1-3) unstable; urgency=low [ Charles Plessy ] Modified: trunk/packages/mira/trunk/debian/compat === --- trunk/packages/mira/trunk/debian/compat 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/compat 2013-06-05 18:10:33 UTC (rev 13848) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/mira/trunk/debian/control === --- trunk/packages/mira/trunk/debian/control2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/control2013-06-05 18:10:33 UTC (rev 13848) @@ -2,14 +2,25 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes -Uploaders: Charles Plessy ple...@debian.org, Steffen Moeller moel...@debian.org, - Tim Booth tbo...@ceh.ac.uk, Andreas Tille ti...@debian.org -Build-Depends: debhelper (= 7.0.50~), autotools-dev, dblatex, docbook-xsl, - libboost-thread-dev, libboost-regex-dev, libexpat1-dev, - libgoogle-perftools-dev [i386 amd64], perl, flex, - vim-common, zlib1g-dev -Standards-Version: 3.9.3 +Uploaders: Charles Plessy ple...@debian.org, + Steffen Moeller moel...@debian.org, + Tim Booth tbo...@ceh.ac.uk, + Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de +Build-Depends: debhelper (= 9), + autotools-dev, + dblatex, + docbook-xsl, + libboost-thread-dev, + libboost-regex-dev, + libboost-iostreams-dev, + libexpat1-dev, + libgoogle-perftools-dev [i386 amd64], + perl, + flex, + vim-common, + zlib1g-dev +Standards-Version: 3.9.4 Homepage: http://chevreux.org/projects_mira.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ Deleted: trunk/packages/mira/trunk/debian/mira-assembler.install === --- trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,8 +0,0 @@ -src/progs/fastatoolusr/bin/ -src/progs/mira usr/bin/ -src/progs/scftool usr/bin/ -src/progs/sw usr/bin/ -src/progs/convert_project usr/bin/ -src/scripts/fasta2frag.tcl usr/bin/ -src/scripts/fastaselect.tclusr/bin/ -src/scripts/fastqselect.tclusr/bin/ Copied: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (from rev 13765, trunk/packages/mira/trunk/debian/mira-assembler.install) === --- trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (rev 0) +++ trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -0,0 +1,8 @@ +#src/progs/fastatool usr/bin/ +#src/progs/mirausr/bin/ +#src/progs/scftool usr/bin/ +#src/progs/sw usr/bin/ +#src/progs/convert_project usr/bin/ +#src/scripts/fasta2frag.tclusr/bin
[med-svn] r13849 - trunk/packages/libzeep/trunk/debian
Author: alteholz Date: 2013-06-05 20:08:47 + (Wed, 05 Jun 2013) New Revision: 13849 Modified: trunk/packages/libzeep/trunk/debian/changelog trunk/packages/libzeep/trunk/debian/control Log: close bug Modified: trunk/packages/libzeep/trunk/debian/changelog === --- trunk/packages/libzeep/trunk/debian/changelog 2013-06-05 18:10:33 UTC (rev 13848) +++ trunk/packages/libzeep/trunk/debian/changelog 2013-06-05 20:08:47 UTC (rev 13849) @@ -1,6 +1,6 @@ libzeep (3.0.1-1) unstable; urgency=low - * New upstream release with fix for IBM S/390 + * New upstream release with fix for IBM S/390 (Closes: #710543) -- Maarten L. Hekkelman m.hekkel...@cmbi.ru.nl Wed, 06 Jun 2013 10:00:00 +0200 Modified: trunk/packages/libzeep/trunk/debian/control === --- trunk/packages/libzeep/trunk/debian/control 2013-06-05 18:10:33 UTC (rev 13848) +++ trunk/packages/libzeep/trunk/debian/control 2013-06-05 20:08:47 UTC (rev 13849) @@ -13,7 +13,6 @@ Section: libs Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libzeep/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libzeep/trunk/ -DM-Upload-Allowed: yes Homepage: http://www.cmbi.ru.nl/libzeep/ Package: libzeep-dev ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13798 - trunk/packages/autodocksuite/trunk/debian
Author: alteholz Date: 2013-06-02 14:02:48 + (Sun, 02 Jun 2013) New Revision: 13798 Added: trunk/packages/autodocksuite/trunk/debian/autodock.lintian-overrides Modified: trunk/packages/autodocksuite/trunk/debian/changelog trunk/packages/autodocksuite/trunk/debian/control trunk/packages/autodocksuite/trunk/debian/rules Log: move package from experimental to unstable Added: trunk/packages/autodocksuite/trunk/debian/autodock.lintian-overrides === --- trunk/packages/autodocksuite/trunk/debian/autodock.lintian-overrides (rev 0) +++ trunk/packages/autodocksuite/trunk/debian/autodock.lintian-overrides 2013-06-02 14:02:48 UTC (rev 13798) @@ -0,0 +1,2 @@ +# In this context Ang means Angstrom +autodock: spelling-error-in-binary usr/bin/autodock4 Ang And Modified: trunk/packages/autodocksuite/trunk/debian/changelog === --- trunk/packages/autodocksuite/trunk/debian/changelog 2013-06-02 09:57:40 UTC (rev 13797) +++ trunk/packages/autodocksuite/trunk/debian/changelog 2013-06-02 14:02:48 UTC (rev 13798) @@ -1,3 +1,12 @@ +autodocksuite (4.2.5.1-3) unstable; urgency=low + + * move package from experimental to unstable + * debian/copntrol: set standard to 3.9.4 (no changes) + * debian/autodock.lintian-overrides: added for wrong spelling error + * debian/rules: add call to dh_lintian + + -- Thorsten Alteholz deb...@alteholz.de Sun, 02 Jun 2013 13:00:00 +0200 + autodocksuite (4.2.5.1-2) experimental; urgency=low * debian/rules: remove lto flags again, does not really work Modified: trunk/packages/autodocksuite/trunk/debian/control === --- trunk/packages/autodocksuite/trunk/debian/control 2013-06-02 09:57:40 UTC (rev 13797) +++ trunk/packages/autodocksuite/trunk/debian/control 2013-06-02 14:02:48 UTC (rev 13798) @@ -8,7 +8,7 @@ Andreas Tille ti...@debian.org, Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 7), automake, csh -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/autodocksuite/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/autodocksuite/trunk/ Homepage: http://autodock.scripps.edu/ Modified: trunk/packages/autodocksuite/trunk/debian/rules === --- trunk/packages/autodocksuite/trunk/debian/rules 2013-06-02 09:57:40 UTC (rev 13797) +++ trunk/packages/autodocksuite/trunk/debian/rules 2013-06-02 14:02:48 UTC (rev 13798) @@ -101,6 +101,7 @@ binary-common: dh_testdir dh_testroot + dh_lintian dh_installchangelogs autodock/RELEASENOTES dh_installdocs dh_installexamples ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13791 - in trunk/packages/mgltools: cmolkit/trunk/debian molkit/trunk/debian
Author: alteholz Date: 2013-06-01 16:12:00 + (Sat, 01 Jun 2013) New Revision: 13791 Modified: trunk/packages/mgltools/cmolkit/trunk/debian/changelog trunk/packages/mgltools/cmolkit/trunk/debian/control trunk/packages/mgltools/molkit/trunk/debian/changelog trunk/packages/mgltools/molkit/trunk/debian/control Log: swig is needed now to build package Modified: trunk/packages/mgltools/cmolkit/trunk/debian/changelog === --- trunk/packages/mgltools/cmolkit/trunk/debian/changelog 2013-06-01 15:17:09 UTC (rev 13790) +++ trunk/packages/mgltools/cmolkit/trunk/debian/changelog 2013-06-01 16:12:00 UTC (rev 13791) @@ -6,6 +6,7 @@ * debian/copyright: add permission for debian to distribute mgltools * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed + * debian/control: add swig to build dependencies -- Thorsten Alteholz deb...@alteholz.de Sun, 19 May 2013 12:00:00 +0200 Modified: trunk/packages/mgltools/cmolkit/trunk/debian/control === --- trunk/packages/mgltools/cmolkit/trunk/debian/control2013-06-01 15:17:09 UTC (rev 13790) +++ trunk/packages/mgltools/cmolkit/trunk/debian/control2013-06-01 16:12:00 UTC (rev 13791) @@ -6,7 +6,7 @@ Uploaders: Steffen Moeller moel...@debian.org, Sargis Dallakyan sar...@scripps.edu, Thorsten Alteholz deb...@alteholz.de -Build-Depends: debhelper (= 8), python-all-dev (= 2.6), python-numpy +Build-Depends: debhelper (= 8), python-all-dev (= 2.6), python-numpy, swig Standards-Version: 3.9.4 XS-Python-Version: = 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/cmolkit/trunk/ Modified: trunk/packages/mgltools/molkit/trunk/debian/changelog === --- trunk/packages/mgltools/molkit/trunk/debian/changelog 2013-06-01 15:17:09 UTC (rev 13790) +++ trunk/packages/mgltools/molkit/trunk/debian/changelog 2013-06-01 16:12:00 UTC (rev 13791) @@ -5,6 +5,7 @@ * debian/copyright: add permission for debian to distribute mgltools * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed + * debian/control: add swig to build dependencies -- Thorsten Alteholz deb...@alteholz.de Sun, 19 May 2013 12:00:00 +0200 Modified: trunk/packages/mgltools/molkit/trunk/debian/control === --- trunk/packages/mgltools/molkit/trunk/debian/control 2013-06-01 15:17:09 UTC (rev 13790) +++ trunk/packages/mgltools/molkit/trunk/debian/control 2013-06-01 16:12:00 UTC (rev 13791) @@ -7,7 +7,7 @@ Sargis Dallakyan sar...@scripps.edu, Andreas Tille ti...@debian.org, Thorsten Alteholz deb...@alteholz.de -Build-Depends: debhelper (= 8), python-all (= 2.6), python-numpy +Build-Depends: debhelper (= 8), python-all (= 2.6), python-numpy, swig Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/molkit/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/molkit/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13792 - trunk/packages/mgltools/cadd/trunk/debian
Author: alteholz Date: 2013-06-01 16:30:17 + (Sat, 01 Jun 2013) New Revision: 13792 Modified: trunk/packages/mgltools/cadd/trunk/debian/changelog trunk/packages/mgltools/cadd/trunk/debian/rules Log: some cadd-files had wrong permissions Modified: trunk/packages/mgltools/cadd/trunk/debian/changelog === --- trunk/packages/mgltools/cadd/trunk/debian/changelog 2013-06-01 16:12:00 UTC (rev 13791) +++ trunk/packages/mgltools/cadd/trunk/debian/changelog 2013-06-01 16:30:17 UTC (rev 13792) @@ -4,6 +4,7 @@ * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed * debian/copyright: add permission for debian to distribute mgltools + * debian/rules: remove x bit from some helper scripts -- Thorsten Alteholz deb...@alteholz.de Sun, 19 May 2013 12:00:00 +0200 Modified: trunk/packages/mgltools/cadd/trunk/debian/rules === --- trunk/packages/mgltools/cadd/trunk/debian/rules 2013-06-01 16:12:00 UTC (rev 13791) +++ trunk/packages/mgltools/cadd/trunk/debian/rules 2013-06-01 16:30:17 UTC (rev 13792) @@ -16,6 +16,8 @@ dh_install find $(CURDIR)/debian/mgltools-cadd -name runCADD | xargs -r chmod 755 find $(CURDIR)/debian/mgltools-cadd -name *.prm -o -name *.res | xargs -r chmod -x + find $(CURDIR)/debian/mgltools-cadd -name raccoonLauncher | xargs -r chmod -x + find $(CURDIR)/debian/mgltools-cadd -name *.bat | xargs -r chmod -x get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13795 - in trunk/packages/saint/trunk/debian: . patches
Author: alteholz Date: 2013-06-01 20:40:44 + (Sat, 01 Jun 2013) New Revision: 13795 Added: trunk/packages/saint/trunk/debian/patches/ld-as-needed.patch Modified: trunk/packages/saint/trunk/debian/changelog trunk/packages/saint/trunk/debian/patches/series Log: small patch for linking as needed Modified: trunk/packages/saint/trunk/debian/changelog === --- trunk/packages/saint/trunk/debian/changelog 2013-06-01 18:09:06 UTC (rev 13794) +++ trunk/packages/saint/trunk/debian/changelog 2013-06-01 20:40:44 UTC (rev 13795) @@ -1,3 +1,9 @@ +saint (2.3.4+dfsg-2) unstable; urgency=low + + * add patch ld-as-needed.patch from Julian Taylor (Closes: #710364) + + -- Thorsten Alteholz deb...@alteholz.de Sat, 01 Jun 2013 22:00:00 +0200 + saint (2.3.4+dfsg-1) unstable; urgency=low * new upstream version Added: trunk/packages/saint/trunk/debian/patches/ld-as-needed.patch === --- trunk/packages/saint/trunk/debian/patches/ld-as-needed.patch (rev 0) +++ trunk/packages/saint/trunk/debian/patches/ld-as-needed.patch 2013-06-01 20:40:44 UTC (rev 13795) @@ -0,0 +1,49 @@ +Description: fix build failure with ld --as-needed + libraries need to be placed after objects needing them +--- a/Makefile b/Makefile +@@ -43,7 +43,7 @@ all: makeDirs \ + saint-reformat: + $(CC) $(CFLAGS) -c $(SRC)/SAINTreformat/*.c $(SRC)/SAINTreformat/*.h + mv *.o $(BUILD) +- $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat ++ $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat $(LIBS) + rm $(BUILD)/*.o + @echo + @echo +@@ -52,7 +52,7 @@ saint-reformat: + saint-spc-noctrl-matrix: + $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl-matrix/*.c $(SRC)/SAINTspc-noctrl-matrix/*.h + mv *.o $(BUILD) +- $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix ++ $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix $(LIBS) + rm $(BUILD)/*.o + @echo + @echo +@@ -60,7 +60,7 @@ saint-spc-noctrl-matrix: + saint-spc-noctrl: + $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl/*.c $(SRC)/SAINTspc-noctrl/*.h + mv *.o $(BUILD) +- $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl ++ $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl $(LIBS) + rm $(BUILD)/*.o + @echo + @echo +@@ -69,7 +69,7 @@ saint-spc-noctrl: + saint-spc-ctrl: + $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-ctrl/*.c $(SRC)/SAINTspc-ctrl/*.h + mv *.o $(BUILD) +- $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl ++ $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-spc-ctrl $(LIBS) + rm $(BUILD)/*.o + @echo + @echo +@@ -78,7 +78,7 @@ saint-spc-ctrl: + saint-int-ctrl: + $(CC) $(CFLAGS) -c $(SRC)/SAINTint-ctrl/*.c $(SRC)/SAINTint-ctrl/*.h + mv *.o $(BUILD) +- $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl ++ $(CC) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-int-ctrl $(LIBS) + rm $(BUILD)/*.o + @echo + @echo Modified: trunk/packages/saint/trunk/debian/patches/series === --- trunk/packages/saint/trunk/debian/patches/series2013-06-01 18:09:06 UTC (rev 13794) +++ trunk/packages/saint/trunk/debian/patches/series2013-06-01 20:40:44 UTC (rev 13795) @@ -1 +1,2 @@ fix-makefile.patch +ld-as-needed.patch ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13796 - trunk/packages/qrisk2/trunk/debian
Author: alteholz Date: 2013-06-01 20:50:18 + (Sat, 01 Jun 2013) New Revision: 13796 Modified: trunk/packages/qrisk2/trunk/debian/changelog Log: new upstream version: QRISK2-2013 release Modified: trunk/packages/qrisk2/trunk/debian/changelog === --- trunk/packages/qrisk2/trunk/debian/changelog2013-06-01 20:40:44 UTC (rev 13795) +++ trunk/packages/qrisk2/trunk/debian/changelog2013-06-01 20:50:18 UTC (rev 13796) @@ -1,8 +1,9 @@ -qrisk2 (0.0.r30-2) UNRELEASED; urgency=low +qrisk2 (0.0.r31-1) unstable; urgency=low - * debian/control: remove . at end of long description (Closes: #705791) + * new upstream version: QRISK2-2013 release + * debian/control: remove . at end of long description (Closes: #705791) - -- Thorsten Alteholz deb...@alteholz.de Mon, 22 Apr 2013 18:00:00 +0200 + -- Thorsten Alteholz deb...@alteholz.de Sat, 01 Jun 2013 22:00:00 +0200 qrisk2 (0.0.r30-1) unstable; urgency=low ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13771 - trunk/packages/libzeep/trunk/debian
Author: alteholz Date: 2013-05-30 17:46:54 + (Thu, 30 May 2013) New Revision: 13771 Modified: trunk/packages/libzeep/trunk/debian/ trunk/packages/libzeep/trunk/debian/changelog trunk/packages/libzeep/trunk/debian/control Log: minor correction Property changes on: trunk/packages/libzeep/trunk/debian ___ Added: mergeWithUpstream + 1 Modified: trunk/packages/libzeep/trunk/debian/changelog === --- trunk/packages/libzeep/trunk/debian/changelog 2013-05-30 14:14:05 UTC (rev 13770) +++ trunk/packages/libzeep/trunk/debian/changelog 2013-05-30 17:46:54 UTC (rev 13771) @@ -1,6 +1,8 @@ libzeep (3.0.0-1) unstable; urgency=low * New upstream release + * debian/control: remove obsolete DM-Upload-Allowed: + * debian/control: set standadrd to 3.9.4 (no changes) -- Maarten L. Hekkelman m.hekkel...@cmbi.ru.nl Wed, 29 May 2013 10:00:00 +0200 Modified: trunk/packages/libzeep/trunk/debian/control === --- trunk/packages/libzeep/trunk/debian/control 2013-05-30 14:14:05 UTC (rev 13770) +++ trunk/packages/libzeep/trunk/debian/control 2013-05-30 17:46:54 UTC (rev 13771) @@ -9,7 +9,7 @@ libboost-regex-dev (= 1.49.0), libboost-math-dev (= 1.49.0), libboost-thread-dev (= 1.49.0) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Section: libs Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libzeep/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libzeep/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13717 - trunk/packages/melting/trunk/debian
Author: alteholz Date: 2013-05-27 19:58:56 + (Mon, 27 May 2013) New Revision: 13717 Modified: trunk/packages/melting/trunk/debian/changelog trunk/packages/melting/trunk/debian/control trunk/packages/melting/trunk/debian/rules trunk/packages/melting/trunk/debian/watch Log: first step to new upstream version Modified: trunk/packages/melting/trunk/debian/changelog === --- trunk/packages/melting/trunk/debian/changelog 2013-05-27 17:41:01 UTC (rev 13716) +++ trunk/packages/melting/trunk/debian/changelog 2013-05-27 19:58:56 UTC (rev 13717) @@ -1,3 +1,11 @@ +melting (5.1.0-1) UNRELEASED; urgency=low + + * new upstream version + * debian/watch: new syntax + * debian/control: bump standard to 3.9.4 (no changes) + + -- Thorsten Alteholz deb...@alteholz.de Sun, 26 May 2013 18:00:00 +0200 + melting (4.3c-2) unstable; urgency=low [ Charles Plessy ] Modified: trunk/packages/melting/trunk/debian/control === --- trunk/packages/melting/trunk/debian/control 2013-05-27 17:41:01 UTC (rev 13716) +++ trunk/packages/melting/trunk/debian/control 2013-05-27 19:58:56 UTC (rev 13717) @@ -4,9 +4,10 @@ Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org DM-Upload-Allowed: yes Uploaders: Charles Plessy ple...@debian.org, - Andreas Tille ti...@debian.org + Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/melting/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/melting/trunk/ Homepage: http://www.ebi.ac.uk/compneur-srv/melting/ Modified: trunk/packages/melting/trunk/debian/rules === --- trunk/packages/melting/trunk/debian/rules 2013-05-27 17:41:01 UTC (rev 13716) +++ trunk/packages/melting/trunk/debian/rules 2013-05-27 19:58:56 UTC (rev 13717) @@ -19,3 +19,8 @@ install -D BIN/tkmelting.pl $(CURDIR)/debian/melting-gui/usr/bin/tkmelting install -m 644 -D BIN/melting.hlp $(CURDIR)/debian/melting-gui/usr/share/melting/melting.hlp install -m 644 -D melting-gui.desktop $(CURDIR)/debian/melting-gui/usr/share/applications/melting-gui.desktop + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Modified: trunk/packages/melting/trunk/debian/watch === --- trunk/packages/melting/trunk/debian/watch 2013-05-27 17:41:01 UTC (rev 13716) +++ trunk/packages/melting/trunk/debian/watch 2013-05-27 19:58:56 UTC (rev 13717) @@ -1,2 +1,3 @@ version=3 -http://sf.net/melting/melting(.*?)_(.*?)\.tar\.gz +opts=uversionmangle=s/_/\./ \ + http://sf.net/melting/MELTING([\d._]*)\.tar\.gz ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13712 - in trunk/packages/python-cogent/trunk/debian: . patches
Author: alteholz
Date: 2013-05-26 16:51:09 + (Sun, 26 May 2013)
New Revision: 13712
Added:
trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base
trunk/packages/python-cogent/trunk/debian/python-cogent-doc.install
Modified:
trunk/packages/python-cogent/trunk/debian/changelog
trunk/packages/python-cogent/trunk/debian/compat
trunk/packages/python-cogent/trunk/debian/control
trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
trunk/packages/python-cogent/trunk/debian/rules
Log:
new upstream version
Modified: trunk/packages/python-cogent/trunk/debian/changelog
===
--- trunk/packages/python-cogent/trunk/debian/changelog 2013-05-25 08:19:49 UTC
(rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/changelog 2013-05-26 16:51:09 UTC
(rev 13712)
@@ -1,11 +1,17 @@
-python-cogent (1.5.3-1) precise; urgency=low
+python-cogent (1.5.3-1) unstable; urgency=low
* New upstream
+ * debian/control: use dh 9
+ * debian/control: set standard to 3.9.4 (no changes)
+ * debian/rules: add get-orig-source target
+ * debian/rules: remove some superfluous files
+
+ [ Tim Booth ]
* Added back python2 helper and invoked dh_numpy to sort deps
* Split out docs into separate package
* Added extra cleanup to dh_clean
- -- Tim Booth tbo...@ceh.ac.uk Tue, 13 Nov 2012 15:26:47 +
+ -- Thorsten Alteholz deb...@alteholz.de Sun, 16 May 2013 18:00:00 +0200
python-cogent (1.5.1-3) UNRELEASED; urgency=low
Modified: trunk/packages/python-cogent/trunk/debian/compat
===
--- trunk/packages/python-cogent/trunk/debian/compat2013-05-25 08:19:49 UTC
(rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/compat2013-05-26 16:51:09 UTC
(rev 13712)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/python-cogent/trunk/debian/control
===
--- trunk/packages/python-cogent/trunk/debian/control 2013-05-25 08:19:49 UTC
(rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/control 2013-05-26 16:51:09 UTC
(rev 13712)
@@ -3,10 +3,11 @@
Priority: extra
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Uploaders: Steffen Moeller moel...@debian.org,
- Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 8), python-all-dev (= 2.6), python-support,
python-numpy (= 1.3.0),
+ Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9), python-all-dev (= 2.6), python-support,
python-numpy (= 1.3.0),
python-sphinx, cython
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Homepage: http://pycogent.sourceforge.net/
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/python-cogent/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-cogent/trunk/
@@ -32,6 +33,12 @@
Section: debug
Depends: python-cogent (= ${binary:Version}), ${misc:Depends}
Description: debug information for pycogent
+ PyCogent is a software library for genomic biology.
+ .
+ It is distinguished by many unique built-in capabilities (such as true codon
+ alignment) and the frequent addition of entirely new methods for the analysis
+ of genomic data.
+ .
This package is needed to improve significantly the bug reports
that users may feel inclined to send.
@@ -41,4 +48,10 @@
Depends: ${misc:Depends}, libjs-jquery, libjs-underscore
Suggests: python-cogent (= ${binary:Version})
Description: docs for python-cogent
- Documentation and examples for python-cogent
+ PyCogent is a software library for genomic biology.
+ .
+ It is distinguished by many unique built-in capabilities (such as true codon
+ alignment) and the frequent addition of entirely new methods for the analysis
+ of genomic data.
+ .
+ This package contains documentation and examples.
Modified:
trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
===
---
trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
2013-05-25 08:19:49 UTC (rev 13711)
+++
trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
2013-05-26 16:51:09 UTC (rev 13712)
@@ -1,3 +1,5 @@
+Author: Steffen Moeller moel...@debian.org
+Description: fix path to python interpreter
Index: PyCogent-1.5.1/cogent/align/dp_calculation.py
===
--- PyCogent-1.5.1.orig/cogent/align/dp_calculation.py 2011-06-06
18:10:17.0 +0200
Added: trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base
===
--- trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base
(rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python
[med-svn] r13680 - in trunk/packages/mgltools: . autodocktools/trunk/debian bhtree/trunk/debian cadd/trunk/debian cmolkit/trunk/debian dejavu/trunk/debian geomutils/trunk/debian gle/trunk/debian mglut
Author: alteholz Date: 2013-05-20 15:23:02 + (Mon, 20 May 2013) New Revision: 13680 Added: trunk/packages/mgltools/TODO Modified: trunk/packages/mgltools/autodocktools/trunk/debian/changelog trunk/packages/mgltools/autodocktools/trunk/debian/control trunk/packages/mgltools/bhtree/trunk/debian/changelog trunk/packages/mgltools/bhtree/trunk/debian/control trunk/packages/mgltools/cadd/trunk/debian/changelog trunk/packages/mgltools/cadd/trunk/debian/control trunk/packages/mgltools/cmolkit/trunk/debian/changelog trunk/packages/mgltools/cmolkit/trunk/debian/control trunk/packages/mgltools/dejavu/trunk/debian/changelog trunk/packages/mgltools/dejavu/trunk/debian/control trunk/packages/mgltools/geomutils/trunk/debian/changelog trunk/packages/mgltools/geomutils/trunk/debian/control trunk/packages/mgltools/gle/trunk/debian/changelog trunk/packages/mgltools/gle/trunk/debian/control trunk/packages/mgltools/mglutil/trunk/debian/changelog trunk/packages/mgltools/mglutil/trunk/debian/control trunk/packages/mgltools/molkit/trunk/debian/changelog trunk/packages/mgltools/molkit/trunk/debian/control trunk/packages/mgltools/mslib/trunk/debian/changelog trunk/packages/mgltools/mslib/trunk/debian/control trunk/packages/mgltools/networkeditor/trunk/debian/changelog trunk/packages/mgltools/networkeditor/trunk/debian/control trunk/packages/mgltools/opengltk/trunk/debian/changelog trunk/packages/mgltools/opengltk/trunk/debian/control trunk/packages/mgltools/opengltk/trunk/debian/patches/series trunk/packages/mgltools/pmv/trunk/debian/changelog trunk/packages/mgltools/pmv/trunk/debian/control trunk/packages/mgltools/pmv/trunk/debian/patches/series trunk/packages/mgltools/pmv/trunk/debian/rules trunk/packages/mgltools/pyautodock/trunk/debian/changelog trunk/packages/mgltools/pyautodock/trunk/debian/control trunk/packages/mgltools/pybabel/trunk/debian/changelog trunk/packages/mgltools/pybabel/trunk/debian/control trunk/packages/mgltools/pyglf/trunk/debian/changelog trunk/packages/mgltools/pyglf/trunk/debian/control trunk/packages/mgltools/qslimlib/trunk/debian/changelog trunk/packages/mgltools/qslimlib/trunk/debian/control trunk/packages/mgltools/qslimlib/trunk/debian/copyright trunk/packages/mgltools/scenario2/trunk/debian/changelog trunk/packages/mgltools/scenario2/trunk/debian/control trunk/packages/mgltools/sff/trunk/debian/changelog trunk/packages/mgltools/sff/trunk/debian/control trunk/packages/mgltools/support/trunk/debian/changelog trunk/packages/mgltools/support/trunk/debian/control trunk/packages/mgltools/symserv/trunk/debian/changelog trunk/packages/mgltools/symserv/trunk/debian/control trunk/packages/mgltools/utpackages/trunk/debian/changelog trunk/packages/mgltools/utpackages/trunk/debian/control trunk/packages/mgltools/viewerframework/trunk/debian/changelog trunk/packages/mgltools/viewerframework/trunk/debian/control trunk/packages/mgltools/viewerframework/trunk/debian/patches/do_not_assign_debug.patch trunk/packages/mgltools/viewerframework/trunk/debian/patches/series trunk/packages/mgltools/vision/trunk/debian/changelog trunk/packages/mgltools/vision/trunk/debian/control trunk/packages/mgltools/visionlibraries/trunk/debian/changelog trunk/packages/mgltools/visionlibraries/trunk/debian/control trunk/packages/mgltools/volume/trunk/debian/changelog trunk/packages/mgltools/volume/trunk/debian/control trunk/packages/mgltools/webservices/trunk/debian/changelog trunk/packages/mgltools/webservices/trunk/debian/control Log: almost done Added: trunk/packages/mgltools/TODO === --- trunk/packages/mgltools/TODO(rev 0) +++ trunk/packages/mgltools/TODO2013-05-20 15:23:02 UTC (rev 13680) @@ -0,0 +1,2 @@ +wait for answer from Michel Sanner about license to distribute and rework debian/copyright - #637430 +(years might have changed) Modified: trunk/packages/mgltools/autodocktools/trunk/debian/changelog === --- trunk/packages/mgltools/autodocktools/trunk/debian/changelog 2013-05-20 13:26:17 UTC (rev 13679) +++ trunk/packages/mgltools/autodocktools/trunk/debian/changelog 2013-05-20 15:23:02 UTC (rev 13680) @@ -1,9 +1,10 @@ -autodocktools (1.5.6-1) unstable; urgency=low +autodocktools (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. * debian/control: bump standard to 3.9.4 (no changes) + * debian/control: remove DM-Upload-Allowed - -- Thorsten Alteholz deb...@alteholz.de Sat, 16 May 2013 12:00:00 +0200 + -- Thorsten Alteholz deb...@alteholz.de Sun, 19 May 2013 12:00:00 +0200 autodocktools (1.5.6~rc3~cvs.20120206-2) UNRELEASED; urgency=low Modified: trunk/packages/mgltools/autodocktools/trunk/debian/control
[med-svn] r13651 - trunk/packages/mgltools/mgltools-external-get-orig-source
Author: alteholz Date: 2013-05-19 16:59:41 + (Sun, 19 May 2013) New Revision: 13651 Modified: trunk/packages/mgltools/mgltools-external-get-orig-source/current-branch trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version Log: should be 1.5.7.RC1 now Modified: trunk/packages/mgltools/mgltools-external-get-orig-source/current-branch === --- trunk/packages/mgltools/mgltools-external-get-orig-source/current-branch 2013-05-19 14:32:32 UTC (rev 13650) +++ trunk/packages/mgltools/mgltools-external-get-orig-source/current-branch 2013-05-19 16:59:41 UTC (rev 13651) @@ -1 +1 @@ -rc-1-5-6 +rc-1-5-7 Modified: trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version === --- trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version 2013-05-19 14:32:32 UTC (rev 13650) +++ trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version 2013-05-19 16:59:41 UTC (rev 13651) @@ -0,0 +1 @@ +~rc1 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13655 - trunk/packages/mgltools/packging_helpers
Author: alteholz Date: 2013-05-19 17:43:08 + (Sun, 19 May 2013) New Revision: 13655 Modified: trunk/packages/mgltools/packging_helpers/svn_buildpackage_all Log: no .svn directory anymore Modified: trunk/packages/mgltools/packging_helpers/svn_buildpackage_all === --- trunk/packages/mgltools/packging_helpers/svn_buildpackage_all 2013-05-19 17:24:56 UTC (rev 13654) +++ trunk/packages/mgltools/packging_helpers/svn_buildpackage_all 2013-05-19 17:43:08 UTC (rev 13655) @@ -17,17 +17,6 @@ echo `dirname $i`: debian directory not found exit fi - if [ ! -d $i/.svn ]; then - echo `dirname $i`: could not find .svn directory - exit - fi - if [ ! -r $i/.svn/deb-layout ]; then - echo `dirname $i`: Creating deb-layout file. - catEOCAT $i/.svn/deb-layout -origDir=../../tarballs -buildArea=../../build-area -EOCAT - fi - (cd $i svn-buildpackage --svn-ignore --svn-reuse --svn-move-to=$moveto) + (cd $i svn-buildpackage --svn-ignore --svn-reuse --svn-move-to=$moveto --svn-override=origDir=../../tarballs,buildArea=../../build-area ) done ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13639 - trunk/packages/mgltools/mgltools-external-get-orig-source
Author: alteholz Date: 2013-05-18 09:48:37 + (Sat, 18 May 2013) New Revision: 13639 Added: trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version.ok Modified: trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version Log: new release Modified: trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version === --- trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version 2013-05-18 09:20:14 UTC (rev 13638) +++ trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version 2013-05-18 09:48:37 UTC (rev 13639) @@ -1 +0,0 @@ -~rc3 Added: trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version.ok === --- trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version.ok (rev 0) +++ trunk/packages/mgltools/mgltools-external-get-orig-source/rc-version.ok 2013-05-18 09:48:37 UTC (rev 13639) @@ -0,0 +1 @@ +~rc3 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13641 - trunk/packages/mgltools/mgltools-external-get-orig-source
Author: alteholz
Date: 2013-05-18 11:52:25 + (Sat, 18 May 2013)
New Revision: 13641
Modified:
trunk/packages/mgltools/mgltools-external-get-orig-source/get-orig-source
Log:
we sometimes have a real release
Modified:
trunk/packages/mgltools/mgltools-external-get-orig-source/get-orig-source
===
--- trunk/packages/mgltools/mgltools-external-get-orig-source/get-orig-source
2013-05-18 11:20:53 UTC (rev 13640)
+++ trunk/packages/mgltools/mgltools-external-get-orig-source/get-orig-source
2013-05-18 11:52:25 UTC (rev 13641)
@@ -55,8 +55,14 @@
if [ -f $MGLTOOLSCVS/build-for-date ]; then
DATE=`cat $MGLTOOLSCVS/build-for-date`
fi
-origFilename=${DEBPACKAGE}_${version}${rcversion}~cvs.${DATE}.orig.tar.gz
-origDirname=${DEBPACKAGE}-${version}${rcversion}~cvs.${DATE}
+if [ -z ${rcversion} ]; then
+ echo I: no rc but real release
+ origFilename=${DEBPACKAGE}_${version}${rcversion}.orig.tar.gz
+ origDirname=${DEBPACKAGE}-${version}${rcversion}
+else
+ origFilename=${DEBPACKAGE}_${version}${rcversion}~cvs.${DATE}.orig.tar.gz
+ origDirname=${DEBPACKAGE}-${version}${rcversion}~cvs.${DATE}
+fi
echo I: Filename of origFile: $origFilename
___
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debian-med-commit@lists.alioth.debian.org
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[med-svn] r13644 - in trunk/packages/mgltools: autodocktools/trunk/debian bhtree/trunk/debian cadd/trunk/debian cmolkit/trunk/debian dejavu/trunk/debian geomutils/trunk/debian gle/trunk/debian mglutil
Author: alteholz Date: 2013-05-18 14:48:35 + (Sat, 18 May 2013) New Revision: 13644 Added: trunk/packages/mgltools/visionlibraries/trunk/debian/mgltools-visionlibraries.lintian-overrides Modified: trunk/packages/mgltools/autodocktools/trunk/debian/changelog trunk/packages/mgltools/bhtree/trunk/debian/changelog trunk/packages/mgltools/bhtree/trunk/debian/control trunk/packages/mgltools/cadd/trunk/debian/changelog trunk/packages/mgltools/cadd/trunk/debian/control trunk/packages/mgltools/cmolkit/trunk/debian/changelog trunk/packages/mgltools/cmolkit/trunk/debian/control trunk/packages/mgltools/cmolkit/trunk/debian/copyright trunk/packages/mgltools/cmolkit/trunk/debian/rules trunk/packages/mgltools/dejavu/trunk/debian/changelog trunk/packages/mgltools/dejavu/trunk/debian/control trunk/packages/mgltools/geomutils/trunk/debian/changelog trunk/packages/mgltools/gle/trunk/debian/changelog trunk/packages/mgltools/mglutil/trunk/debian/changelog trunk/packages/mgltools/mglutil/trunk/debian/control trunk/packages/mgltools/molkit/trunk/debian/changelog trunk/packages/mgltools/molkit/trunk/debian/control trunk/packages/mgltools/molkit/trunk/debian/copyright trunk/packages/mgltools/mslib/trunk/debian/changelog trunk/packages/mgltools/networkeditor/trunk/debian/changelog trunk/packages/mgltools/networkeditor/trunk/debian/control trunk/packages/mgltools/opengltk/trunk/debian/changelog trunk/packages/mgltools/packging_helpers/svn_buildpackage_all trunk/packages/mgltools/pmv/trunk/debian/changelog trunk/packages/mgltools/pyautodock/trunk/debian/changelog trunk/packages/mgltools/pyautodock/trunk/debian/control trunk/packages/mgltools/pybabel/trunk/debian/changelog trunk/packages/mgltools/pybabel/trunk/debian/control trunk/packages/mgltools/pyglf/trunk/debian/changelog trunk/packages/mgltools/qslimlib/trunk/debian/changelog trunk/packages/mgltools/qslimlib/trunk/debian/control trunk/packages/mgltools/qslimlib/trunk/debian/copyright trunk/packages/mgltools/qslimlib/trunk/debian/rules trunk/packages/mgltools/scenario2/trunk/debian/changelog trunk/packages/mgltools/scenario2/trunk/debian/control trunk/packages/mgltools/sff/trunk/debian/changelog trunk/packages/mgltools/support/trunk/debian/changelog trunk/packages/mgltools/symserv/trunk/debian/changelog trunk/packages/mgltools/symserv/trunk/debian/control trunk/packages/mgltools/utpackages/trunk/debian/changelog trunk/packages/mgltools/viewerframework/trunk/debian/changelog trunk/packages/mgltools/viewerframework/trunk/debian/control trunk/packages/mgltools/vision/trunk/debian/changelog trunk/packages/mgltools/visionlibraries/trunk/debian/changelog trunk/packages/mgltools/volume/trunk/debian/changelog trunk/packages/mgltools/volume/trunk/debian/control trunk/packages/mgltools/webservices/trunk/debian/changelog trunk/packages/mgltools/webservices/trunk/debian/control Log: first part of mgltools update Modified: trunk/packages/mgltools/autodocktools/trunk/debian/changelog === --- trunk/packages/mgltools/autodocktools/trunk/debian/changelog 2013-05-18 12:11:35 UTC (rev 13643) +++ trunk/packages/mgltools/autodocktools/trunk/debian/changelog 2013-05-18 14:48:35 UTC (rev 13644) @@ -1,3 +1,10 @@ +autodocktools (1.5.6-1) unstable; urgency=low + + * New upstream version. + * debian/control: bump standard to 3.9.4 (no changes) + + -- Thorsten Alteholz deb...@alteholz.de Sat, 16 May 2013 12:00:00 +0200 + autodocktools (1.5.6~rc3~cvs.20120206-2) UNRELEASED; urgency=low * debian/upstream: Enhanced citation information Modified: trunk/packages/mgltools/bhtree/trunk/debian/changelog === --- trunk/packages/mgltools/bhtree/trunk/debian/changelog 2013-05-18 12:11:35 UTC (rev 13643) +++ trunk/packages/mgltools/bhtree/trunk/debian/changelog 2013-05-18 14:48:35 UTC (rev 13644) @@ -1,3 +1,9 @@ +mgltools-bhtree (1.5.6-1) unstable; urgency=low + + * New upstream version. + + -- Thorsten Alteholz deb...@alteholz.de Sat, 16 May 2013 12:00:00 +0200 + mgltools-bhtree (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low * New upstream version. Modified: trunk/packages/mgltools/bhtree/trunk/debian/control === --- trunk/packages/mgltools/bhtree/trunk/debian/control 2013-05-18 12:11:35 UTC (rev 13643) +++ trunk/packages/mgltools/bhtree/trunk/debian/control 2013-05-18 14:48:35 UTC (rev 13644) @@ -9,7 +9,7 @@ Andreas Tille ti...@debian.org, Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 8), python-all-dev (= 2.6), python-numpy, swig (= 1.3.20) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 XS-Python-Version: = 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/bhtree
[med-svn] r13604 - in trunk/packages/epigrass/trunk/debian: . patches
Author: alteholz
Date: 2013-05-16 15:06:14 + (Thu, 16 May 2013)
New Revision: 13604
Added:
trunk/packages/epigrass/trunk/debian/epigrass-doc.doc-base
Modified:
trunk/packages/epigrass/trunk/debian/changelog
trunk/packages/epigrass/trunk/debian/compat
trunk/packages/epigrass/trunk/debian/control
trunk/packages/epigrass/trunk/debian/copyright
trunk/packages/epigrass/trunk/debian/patches/sqlite3.diff
trunk/packages/epigrass/trunk/debian/rules
Log:
new version of epigrass
Modified: trunk/packages/epigrass/trunk/debian/changelog
===
--- trunk/packages/epigrass/trunk/debian/changelog 2013-05-16 13:42:57 UTC
(rev 13603)
+++ trunk/packages/epigrass/trunk/debian/changelog 2013-05-16 15:06:14 UTC
(rev 13604)
@@ -1,3 +1,16 @@
+epigrass (2.2.2-1) unstable; urgency=low
+
+ * new upstream version
+ * debian/control: Standards-Version: 3.9.4 (no changes needed)
+ * debian/control: swith to dh 9
+ * debian/rules: make get-orig-source compatible with svn-buildpackage
+ * debian/control: remove duplicate Depends: on python-visual
+ * debian/control: remove dependency on quilt
+ * debian/control: add new dependency on python-visual
+ * debian/copyright: add correct Format: line
+
+ -- Thorsten Alteholz deb...@alteholz.de Sun, 12 May 2013 18:00:00 +0200
+
epigrass (2.0.4-3) unstable; urgency=low
* debian/control: Homepage has changed to
Modified: trunk/packages/epigrass/trunk/debian/compat
===
--- trunk/packages/epigrass/trunk/debian/compat 2013-05-16 13:42:57 UTC (rev
13603)
+++ trunk/packages/epigrass/trunk/debian/compat 2013-05-16 15:06:14 UTC (rev
13604)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/epigrass/trunk/debian/control
===
--- trunk/packages/epigrass/trunk/debian/control2013-05-16 13:42:57 UTC
(rev 13603)
+++ trunk/packages/epigrass/trunk/debian/control2013-05-16 15:06:14 UTC
(rev 13604)
@@ -5,10 +5,11 @@
Uploaders: Torsten Werner twer...@debian.org,
Varun Hiremath va...@debian.org,
Charles Plessy ple...@debian.org,
- Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 8), python (= 2.6),
- python-setuptools, python-support, quilt, python-virtualenv
-Standards-Version: 3.9.2
+ Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9), python (= 2.6),
+ python-setuptools, python-support, python-virtualenv
+Standards-Version: 3.9.4
Homepage: http://pypi.python.org/pypi/epigrass/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/epigrass/trunk/
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/epigrass/trunk/
@@ -17,8 +18,9 @@
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
python-sqlobject (= 0.12.4-2), python-visual, python-qt4-gl, python-qwt5-qt4
(= 5.2.0),
- python-numpy, python-gdal, python-visual, python-formencode, python-mysqldb,
- python-pysqlite2, python-matplotlib, python-networkx, python-pkg-resources
+ python-numpy, python-gdal, python-formencode, python-mysqldb,
+ python-pysqlite2, python-matplotlib, python-networkx, python-pkg-resources,
+ python-sqlalchemy
Suggests: grass, epigrass-doc
Description: scientific tool for simulations and scenario analysis in network
epidemiology
Epigrass is a software for visualizing, analyzing and simulating of
Modified: trunk/packages/epigrass/trunk/debian/copyright
===
--- trunk/packages/epigrass/trunk/debian/copyright 2013-05-16 13:42:57 UTC
(rev 13603)
+++ trunk/packages/epigrass/trunk/debian/copyright 2013-05-16 15:06:14 UTC
(rev 13604)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: EpiGrass
Upstream-Contact: Flávio Codeço Coelho fccoe...@fiocruz.br,
Cláudia Torres Codeço cod...@fiocruz.br
@@ -31,4 +31,5 @@
© 2007, Torsten Werner twer...@debian.org
© 2008–2009, Charles Plessy ple...@debian.org
© 2009-2011, Andreas Tille ti...@debian.org
+ © 2013, Thorsten Alteholz deb...@alteholz.de
License: GPL-2+
Added: trunk/packages/epigrass/trunk/debian/epigrass-doc.doc-base
===
--- trunk/packages/epigrass/trunk/debian/epigrass-doc.doc-base
(rev 0)
+++ trunk/packages/epigrass/trunk/debian/epigrass-doc.doc-base 2013-05-16
15:06:14 UTC (rev 13604)
@@ -0,0 +1,12 @@
+Document: epigrass
+Title: Epigrass Documentation
+Author: Flavio Codeco Coelho
+Abstract: Epigrass is a framework for the construction and simulation
+ of complex network epidemiology models. At least this is its main
+ vocation. However
[med-svn] r13609 - in trunk/packages/saint/trunk/debian: . patches
Author: alteholz
Date: 2013-05-16 20:03:26 + (Thu, 16 May 2013)
New Revision: 13609
Modified:
trunk/packages/saint/trunk/debian/
trunk/packages/saint/trunk/debian/changelog
trunk/packages/saint/trunk/debian/control
trunk/packages/saint/trunk/debian/get-orig-source
trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
trunk/packages/saint/trunk/debian/saint-int-ctrl.1
Log:
new upstream version
Property changes on: trunk/packages/saint/trunk/debian
___
Added: mergeWithUpstream
+ 1
Modified: trunk/packages/saint/trunk/debian/changelog
===
--- trunk/packages/saint/trunk/debian/changelog 2013-05-16 16:28:44 UTC (rev
13608)
+++ trunk/packages/saint/trunk/debian/changelog 2013-05-16 20:03:26 UTC (rev
13609)
@@ -1,9 +1,13 @@
-saint (2.3.3+dfsg-1) UNRELEASED; urgency=low
+saint (2.3.4+dfsg-1) unstable; urgency=low
+ * new upstream version
+ * debian/control: bump standard to 3.9.4 (no changes needed)
+
+ [Andreas Tille]
* debian/copyright:
- Add Files-Excluded to document what was removed from original source
- -- Andreas Tille ti...@debian.org Fri, 24 Aug 2012 16:20:26 +0200
+ -- Thorsten Alteholz deb...@alteholz.de Thu, 16 May 2013 21:20:00 +0200
saint (2.3.3-1) unstable; urgency=low
Modified: trunk/packages/saint/trunk/debian/control
===
--- trunk/packages/saint/trunk/debian/control 2013-05-16 16:28:44 UTC (rev
13608)
+++ trunk/packages/saint/trunk/debian/control 2013-05-16 20:03:26 UTC (rev
13609)
@@ -2,9 +2,10 @@
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
-Uploaders: Andreas Tille ti...@debian.org
+Uploaders: Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
Build-Depends: debhelper (= 9), libgsl0-dev
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Homepage: http://saint-apms.sourceforge.net/Main.html
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/saint/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/saint/trunk/
Modified: trunk/packages/saint/trunk/debian/get-orig-source
===
--- trunk/packages/saint/trunk/debian/get-orig-source 2013-05-16 16:28:44 UTC
(rev 13608)
+++ trunk/packages/saint/trunk/debian/get-orig-source 2013-05-16 20:03:26 UTC
(rev 13609)
@@ -30,5 +30,5 @@
find ${upstream} -name *.c -type f -exec chmod a-x \{\} \;
find ${upstream} -name *.h -type f -exec chmod a-x \{\} \;
-GZIP=--best --no-name tar --owner=root --group=root --mode=a+rX -czf
$NAME_$VERSION.orig.tar.gz ${upstream}
+GZIP=--best --no-name tar --owner=root --group=root --mode=a+rX -czf
$NAME_$VERSION+dfsg.orig.tar.gz ${upstream}
rm -rf $upstream
Modified: trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
===
--- trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
2013-05-16 16:28:44 UTC (rev 13608)
+++ trunk/packages/saint/trunk/debian/patches/fix-makefile.patch
2013-05-16 20:03:26 UTC (rev 13609)
@@ -1,5 +1,20 @@
SAINT_v2.3.3.orig/Makefile
-+++ SAINT_v2.3.3/Makefile
+Author: Thorsten Alteholz + Andreas Tille
+Description: add hardening flags to makefile and fix clean target
+Index: SAINT_v2.3.4/Makefile
+===
+--- SAINT_v2.3.4.orig/Makefile 2013-05-16 21:11:02.0 +0200
SAINT_v2.3.4/Makefile 2013-05-16 21:12:28.0 +0200
+@@ -14,8 +14,8 @@
+
+ CC = gcc
+ CXX = g++
+-CFLAGS = -g -O3
+-CXXFLAGS = $(CFLAGS)
++CFLAGS += -g -O3
++CXXFLAGS += $(CFLAGS)
+
+
#-
+ # any extra libraries we wish to link with the projects
@@ -29,7 +29,7 @@
clean:
@@ -9,3 +24,48 @@
all: makeDirs \
saint-reformat \
+@@ -43,7 +43,7 @@
+ saint-reformat:
+ $(CC) $(CFLAGS) -c $(SRC)/SAINTreformat/*.c $(SRC)/SAINTreformat/*.h
+ mv *.o $(BUILD)
+- $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-reformat
++ $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o $(TARGET)/saint-reformat
+ rm $(BUILD)/*.o
+ @echo
+ @echo
+@@ -52,7 +52,7 @@
+ saint-spc-noctrl-matrix:
+ $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl-matrix/*.c
$(SRC)/SAINTspc-noctrl-matrix/*.h
+ mv *.o $(BUILD)
+- $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl-matrix
++ $(CC) $(LIBS) $(LDFLAGS) $(BUILD)/*.o -o
$(TARGET)/saint-spc-noctrl-matrix
+ rm $(BUILD)/*.o
+ @echo
+ @echo
+@@ -60,7 +60,7 @@
+ saint-spc-noctrl:
+ $(CC) $(CFLAGS) -c $(SRC)/SAINTspc-noctrl/*.c $(SRC)/SAINTspc-noctrl/*.h
+ mv *.o $(BUILD)
+- $(CC) $(LIBS) $(BUILD)/*.o -o $(TARGET)/saint-spc-noctrl
[med-svn] r13507 - trunk/packages/fasttree/trunk/debian
Author: alteholz Date: 2013-05-06 17:35:02 + (Mon, 06 May 2013) New Revision: 13507 Modified: trunk/packages/fasttree/trunk/debian/changelog trunk/packages/fasttree/trunk/debian/control Log: new version Modified: trunk/packages/fasttree/trunk/debian/changelog === --- trunk/packages/fasttree/trunk/debian/changelog 2013-05-06 07:39:14 UTC (rev 13506) +++ trunk/packages/fasttree/trunk/debian/changelog 2013-05-06 17:35:02 UTC (rev 13507) @@ -1,3 +1,11 @@ +fasttree (2.1.7-1) unstable; urgency=low + + * New upstream version + * debian/control: remove DM-Upload-Allowed: + * debian/control: bump standards version to 3.9.4 + + -- Thorsten Alteholz deb...@alteholz.de Mon, 06 May 2013 18:00:00 +0200 + fasttree (2.1.5-1) unstable; urgency=low * New upstream version Modified: trunk/packages/fasttree/trunk/debian/control === --- trunk/packages/fasttree/trunk/debian/control2013-05-06 07:39:14 UTC (rev 13506) +++ trunk/packages/fasttree/trunk/debian/control2013-05-06 17:35:02 UTC (rev 13507) @@ -2,12 +2,11 @@ Section: science Priority: extra Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes Uploaders: Steffen Moeller moel...@debian.org, Thorsten Alteholz deb...@alteholz.de, Andreas Tille ti...@debian.org Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://www.microbesonline.org/fasttree/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13482 - trunk/packages/gnuhealth/trunk/debian
Author: alteholz Date: 2013-05-04 13:02:21 + (Sat, 04 May 2013) New Revision: 13482 Modified: trunk/packages/gnuhealth/trunk/debian/rules Log: add get-orig-source target Modified: trunk/packages/gnuhealth/trunk/debian/rules === --- trunk/packages/gnuhealth/trunk/debian/rules 2013-05-03 21:59:59 UTC (rev 13481) +++ trunk/packages/gnuhealth/trunk/debian/rules 2013-05-04 13:02:21 UTC (rev 13482) @@ -34,3 +34,7 @@ override_dh_builddeb: dh_builddeb -- -Zxz + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13470 - in trunk/packages/proalign/trunk/debian: . scripts
Author: alteholz
Date: 2013-05-02 17:49:18 + (Thu, 02 May 2013)
New Revision: 13470
Added:
trunk/packages/proalign/trunk/debian/proalign.1
trunk/packages/proalign/trunk/debian/proalign.manpages
Modified:
trunk/packages/proalign/trunk/debian/changelog
trunk/packages/proalign/trunk/debian/control
trunk/packages/proalign/trunk/debian/rules
trunk/packages/proalign/trunk/debian/scripts/proalign
Log:
ready for upload
Modified: trunk/packages/proalign/trunk/debian/changelog
===
--- trunk/packages/proalign/trunk/debian/changelog 2013-05-02 17:09:17 UTC
(rev 13469)
+++ trunk/packages/proalign/trunk/debian/changelog 2013-05-02 17:49:18 UTC
(rev 13470)
@@ -1,4 +1,4 @@
-proalign (0.603-1) UNRELEASED; urgency=low
+proalign (0.603-1) unstable; urgency=low
* Initial release (Closes: #378290)
Modified: trunk/packages/proalign/trunk/debian/control
===
--- trunk/packages/proalign/trunk/debian/control2013-05-02 17:09:17 UTC
(rev 13469)
+++ trunk/packages/proalign/trunk/debian/control2013-05-02 17:49:18 UTC
(rev 13470)
@@ -5,7 +5,8 @@
DM-Upload-Allowed: yes
Uploaders: Andreas Tille ti...@debian.org,
Thorsten Alteholz deb...@alteholz.de
-Build-Depends: debhelper (= 9)
+Build-Depends: debhelper (= 9),
+ default-jdk
Standards-Version: 3.9.4
Homepage: http://ueg.ulb.ac.be/ProAlign/
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/
@@ -13,7 +14,8 @@
Package: proalign
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ default-jre
Description: Probabilistic multiple alignment program
ProAlign performs probabilistic sequence alignments using hidden Markov
models (HMM). It includes a graphical interface (GUI) allowing to (i)
Added: trunk/packages/proalign/trunk/debian/proalign.1
===
--- trunk/packages/proalign/trunk/debian/proalign.1
(rev 0)
+++ trunk/packages/proalign/trunk/debian/proalign.1 2013-05-02 17:49:18 UTC
(rev 13470)
@@ -0,0 +1,79 @@
+.TH PROALIGN 1 May 2013 ProAlign User Commands
+.SH NAME
+proalign \- a probabilistic multiple alignment program
+.SH SYNOPSIS
+.B proalign [OPTIONS]
+.SH DESCRIPTION
+Only limited usage of the program is possible from command line.
+Better use version with GUI (start without OPTIONS).
+.SH OPTIONS
+.TP
+\fB\-nogui\fR
+force command line
+.TP
+\fB-seqfile=sequence file\fR
+.TP
+\fB-treefile=tree file\fR
+.TP
+\fB-newtree \fR
+compute a new guide tree
+.TP
+\fB-sample \fR
+sample traceback path; if not given, Viterbi is chosen
+.TP
+\fB-delta=HMM delta or \-delta=estimate \fR
+if not given, default is used
+.TP
+\fB-epsilon=HMM epsilon or \-epsilon=estimate \fR
+if not given, default is used
+.TP
+\fB-gapfreq=gap frequency \fR
+if not given, default is used
+.TP
+\fB-gapprob=gap substitution probability \fR
+if not given, default is used
+.TP
+\fB-bwidth=search band width \fR
+if not given, default is used
+.TP
+\fB-distscale=distance scale factor \fR
+for branch lengths
+.TP
+\fB-nocorrection \fR
+no correction for pairwise distances on guide tree computation
+.TP
+\fB-notrailing \fR
+no trailing sequence corrcection
+.TP
+\fB-trailing=trailing sequence correction length \fR
+for missing ends
+.TP
+\fB-penalize=true, or =false \fR
+penalize end gaps on pairwise alignments for guide tree
+.TP
+\fB-writemean \fR
+write mean posterior probability of sites
+.TP
+\fB-writeall \fR
+write posterior probability of each node
+.TP
+\fB-writeroot \fR
+write root node character probabilities
+.TP
+\fB-wag \fR
+use WAG probability table
+.TP
+\fB-dayhoff \fR
+use Dayhoff probability table
+.TP
+\fB-jtt \fR
+use JTT probability table
+.TP
+\fB-outfile=alignment file\fR
+.TP
+\fB\-outformat=pir, \-outformat=msf, \-outformat=phylip, or \-outformat=nexus
\fR
+output format
+.TP
+\fB-quiet \fR
+no log
+
Added: trunk/packages/proalign/trunk/debian/proalign.manpages
===
--- trunk/packages/proalign/trunk/debian/proalign.manpages
(rev 0)
+++ trunk/packages/proalign/trunk/debian/proalign.manpages 2013-05-02
17:49:18 UTC (rev 13470)
@@ -0,0 +1 @@
+debian/proalign.1
Modified: trunk/packages/proalign/trunk/debian/rules
===
--- trunk/packages/proalign/trunk/debian/rules 2013-05-02 17:09:17 UTC (rev
13469)
+++ trunk/packages/proalign/trunk/debian/rules 2013-05-02 17:49:18 UTC (rev
13470)
@@ -8,15 +8,9 @@
override_dh_auto_build:
mkdir -p build
javac -d ./build *.java
- find
(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *)
#(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar
proalign/ProAlign.class proalign
[med-svn] r13468 - in trunk/packages/proalign/trunk/debian: . scripts source
Author: alteholz Date: 2013-05-01 20:09:53 + (Wed, 01 May 2013) New Revision: 13468 Added: trunk/packages/proalign/trunk/debian/manifest.txt trunk/packages/proalign/trunk/debian/proalign.install trunk/packages/proalign/trunk/debian/rules trunk/packages/proalign/trunk/debian/scripts/ trunk/packages/proalign/trunk/debian/scripts/proalign trunk/packages/proalign/trunk/debian/source/ trunk/packages/proalign/trunk/debian/source/format Modified: trunk/packages/proalign/trunk/debian/ trunk/packages/proalign/trunk/debian/changelog trunk/packages/proalign/trunk/debian/control trunk/packages/proalign/trunk/debian/watch Log: proalign almost ready, just needs a manpage and some tests Property changes on: trunk/packages/proalign/trunk/debian ___ Added: mergeWithUpstream + 1 Modified: trunk/packages/proalign/trunk/debian/changelog === --- trunk/packages/proalign/trunk/debian/changelog 2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/changelog 2013-05-01 20:09:53 UTC (rev 13468) @@ -1,5 +1,5 @@ -proalign (0.603-1) unstable; urgency=low +proalign (0.603-1) UNRELEASED; urgency=low * Initial release (Closes: #378290) - -- Andreas Tille ti...@debian.org Thu, 24 May 2012 14:30:13 +0200 + -- Thorsten Alteholz deb...@alteholz.de Tue, 01 May 2013 18:00:00 +0200 Modified: trunk/packages/proalign/trunk/debian/control === --- trunk/packages/proalign/trunk/debian/control2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/control2013-05-01 20:09:53 UTC (rev 13468) @@ -3,9 +3,10 @@ Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org DM-Upload-Allowed: yes -Uploaders: Andreas Tille ti...@debian.org +Uploaders: Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://ueg.ulb.ac.be/ProAlign/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/ @@ -18,11 +19,11 @@ models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and - (iv) export alignments to other softwares. + (iv) export alignments to other software. . ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different - characters according to an evolutionary model. \ No newline at end of file + characters according to an evolutionary model. Added: trunk/packages/proalign/trunk/debian/manifest.txt === --- trunk/packages/proalign/trunk/debian/manifest.txt (rev 0) +++ trunk/packages/proalign/trunk/debian/manifest.txt 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +Manifest-version: 1.0 +Main-Class: proalign.ProAlign + Added: trunk/packages/proalign/trunk/debian/proalign.install === --- trunk/packages/proalign/trunk/debian/proalign.install (rev 0) +++ trunk/packages/proalign/trunk/debian/proalign.install 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +debian/scripts/proalign usr/bin +build/ProAlign.jar usr/share/proalign + Added: trunk/packages/proalign/trunk/debian/rules === --- trunk/packages/proalign/trunk/debian/rules (rev 0) +++ trunk/packages/proalign/trunk/debian/rules 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ + +override_dh_auto_build: + mkdir -p build + javac -d ./build *.java + find + (cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *) + #(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class) + +override_dh_auto_install: + find + dh_auto_install + #dh_installchangelogs README + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Property changes on: trunk/packages/proalign/trunk/debian/rules ___ Added: svn:executable + * Added: trunk/packages/proalign/trunk
[med-svn] r13446 - in trunk/packages/ecell/trunk/debian: . source
Author: alteholz
Date: 2013-04-30 20:28:23 + (Tue, 30 Apr 2013)
New Revision: 13446
Added:
trunk/packages/ecell/trunk/debian/source/
trunk/packages/ecell/trunk/debian/source/format
Modified:
trunk/packages/ecell/trunk/debian/changelog
trunk/packages/ecell/trunk/debian/compat
trunk/packages/ecell/trunk/debian/control
trunk/packages/ecell/trunk/debian/rules
Log:
some progress until boost errors occured
Modified: trunk/packages/ecell/trunk/debian/changelog
===
--- trunk/packages/ecell/trunk/debian/changelog 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/changelog 2013-04-30 20:28:23 UTC (rev
13446)
@@ -4,6 +4,7 @@
* TODO: check dependencies:
- is it correct to replace python2.2-xmlbase by python?
- is it correct to replace python2.2-numeric by python-numpy?
+ * TODO: take care of boost compile errors
[ Thorsten Alteholz ]
* new upstream version
Modified: trunk/packages/ecell/trunk/debian/compat
===
--- trunk/packages/ecell/trunk/debian/compat2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/compat2013-04-30 20:28:23 UTC (rev
13446)
@@ -1 +1 @@
-4
+9
Modified: trunk/packages/ecell/trunk/debian/control
===
--- trunk/packages/ecell/trunk/debian/control 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/control 2013-04-30 20:28:23 UTC (rev
13446)
@@ -4,13 +4,35 @@
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller moel...@pzr.uni-rostock.de
-Build-Depends: debhelper (= 4.0.0), python-numpy, python-dev, python-gtk2,
python-glade2, g++ (= 3.3), libgsl0-dev, libboost-python-dev, automake,
autoconf, libtool, python-gnome2, expect, doxygen, graphviz, docbook-utils,
ghostscript, docbook-to-man
+Build-Depends: debhelper (= 9),
+ python-numpy,
+ python-dev,
+ python-gtk2,
+ python-glade2,
+ g++ (= 3.3),
+ libgsl0-dev,
+ libboost-python-dev,
+ automake,
+ autoconf,
+ libtool,
+ python-gnome2,
+ python-ply,
+ expect,
+ doxygen,
+ graphviz,
+ docbook-utils,
+ ghostscript,
+ docbook-to-man
Standards-Version: 3.6.0
Homepage: http://www.e-cell.org/
Package: ecell
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libgsl0, libgnome2-0,
python-numpy, python-glade2
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libgsl0,
+ libgnome2-0,
+ python-numpy,
+ python-glade2
Description: Concept and environment for constructing virtual cells on
computers
The E-Cell Project is an international research project aiming at
developing necessary theoretical supports, technologies and software
Modified: trunk/packages/ecell/trunk/debian/rules
===
--- trunk/packages/ecell/trunk/debian/rules 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/rules 2013-04-30 20:28:23 UTC (rev
13446)
@@ -9,17 +9,10 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-# This has to be exported to make some magic below work.
-export DH_OPTIONS
-
-# 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 ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-CFLAGS = -Wall -g
-
+CFLAGS += -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
else
@@ -29,126 +22,168 @@
INSTALL_PROGRAM += -s
endif
-configure: configure.in
- dh_testdir
+
+%:
+ dh $@
+
+override_dh_auto_configure:
./autogen.sh --enable-static=no --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info
-
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
CFLAGS=$(CFLAGS) ./configure --enable-static=no
--host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr
--mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
#CFLAGS=$(CFLAGS) ./configure --disable-gtk
--host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr
--mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
-#Architecture
-build: ecell.1 build-arch build-indep
-
-build-arch: build-arch-stamp
-build-arch-stamp: config.status
-
- # Add here commands to compile the arch part of the package.
- $(MAKE)
- touch build-arch-stamp
-
-build-indep: build-indep-stamp
-build-indep-stamp: config.status
-
- # Add here commands to compile the indep part of the package.
+override_dh_auto_build:
$(MAKE) doc
- touch
[med-svn] r13438 - in trunk/packages: . thera-pi thera-pi/trunk thera-pi/trunk/debian thera-pi/trunk/debian/source
Author: alteholz
Date: 2013-04-29 17:53:33 + (Mon, 29 Apr 2013)
New Revision: 13438
Added:
trunk/packages/thera-pi/
trunk/packages/thera-pi/trunk/
trunk/packages/thera-pi/trunk/README.status
trunk/packages/thera-pi/trunk/debian/
trunk/packages/thera-pi/trunk/debian/TODO
trunk/packages/thera-pi/trunk/debian/changelog
trunk/packages/thera-pi/trunk/debian/compat
trunk/packages/thera-pi/trunk/debian/control
trunk/packages/thera-pi/trunk/debian/get-orig-source
trunk/packages/thera-pi/trunk/debian/rules
trunk/packages/thera-pi/trunk/debian/source/
trunk/packages/thera-pi/trunk/debian/source/format
trunk/packages/thera-pi/trunk/debian/watch
Log:
first draft
Added: trunk/packages/thera-pi/trunk/README.status
===
--- trunk/packages/thera-pi/trunk/README.status (rev 0)
+++ trunk/packages/thera-pi/trunk/README.status 2013-04-29 17:53:33 UTC (rev
13438)
@@ -0,0 +1,6 @@
+---
+Format: 1
+Status: draft
+Comment:
+ One need to take care of lots of libraries.
+ This might be a rather time-consuming task.
Property changes on: trunk/packages/thera-pi/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/thera-pi/trunk/debian/TODO
===
--- trunk/packages/thera-pi/trunk/debian/TODO (rev 0)
+++ trunk/packages/thera-pi/trunk/debian/TODO 2013-04-29 17:53:33 UTC (rev
13438)
@@ -0,0 +1,9 @@
+TODO:
+=
+
+- most of build.xml do not really work out of the box
+- directory Library contains about 65 jar files that need to be replaced
+ by the Debian libraries
+- debian/copyright
+- man page
+(...)
Added: trunk/packages/thera-pi/trunk/debian/changelog
===
--- trunk/packages/thera-pi/trunk/debian/changelog
(rev 0)
+++ trunk/packages/thera-pi/trunk/debian/changelog 2013-04-29 17:53:33 UTC
(rev 13438)
@@ -0,0 +1,5 @@
+thera-pi (0.0.0.20130429-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #XX)
+
+ -- DPMT debian-med-packag...@lists.alioth.debian.org Thu, 18 Apr 2013
18:00:00 +0200
Added: trunk/packages/thera-pi/trunk/debian/compat
===
--- trunk/packages/thera-pi/trunk/debian/compat (rev 0)
+++ trunk/packages/thera-pi/trunk/debian/compat 2013-04-29 17:53:33 UTC (rev
13438)
@@ -0,0 +1 @@
+9
Added: trunk/packages/thera-pi/trunk/debian/control
===
--- trunk/packages/thera-pi/trunk/debian/control
(rev 0)
+++ trunk/packages/thera-pi/trunk/debian/control2013-04-29 17:53:33 UTC
(rev 13438)
@@ -0,0 +1,20 @@
+Source: thera-pi
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9),
+ default-jdk
+Standards-Version: 3.9.4
+Homepage: http://www.thera-pi.org/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qrisk2/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qrisk2/trunk/
+
+Package: thera-pi
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ default-jre
+Description: organization and management of outpatient clinics and
rehabilitation-medicine companies
+ This project targets at the German health care system.
+
Added: trunk/packages/thera-pi/trunk/debian/get-orig-source
===
--- trunk/packages/thera-pi/trunk/debian/get-orig-source
(rev 0)
+++ trunk/packages/thera-pi/trunk/debian/get-orig-source2013-04-29
17:53:33 UTC (rev 13438)
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+PACKAGE=thera-pi
+PACKAGEVERSION=`dpkg-parsechangelog | sed -n -e 's/^Version:
\(.*\)-[^-]*$/\1/p'`
+declare -i CHANGELOGREVISION=`echo ${PACKAGEVERSION}|awk -F. '{print
$4}'|awk -F- '{print $1}'`
+TODAYVERSION=0.0.0.`date +%Y%m%d`
+echo I: anonymous cvs access, just hit enter
+cvs -d:pserver:anonym...@thera-pi.cvs.sourceforge.net:/cvsroot/thera-pi login
+
+echo I: package version: ${PACKAGEVERSION}
+echo I: version today: ${TODAYVERSION}
+echo I: version from changelog: ${CHANGELOGREVISION}
+
+FOLDER=${PACKAGE}_${TODAYVERSION}
+TARFILE=${FOLDER}.orig.tar.gz
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+# we have cvs here and need to checkout stuff to get the list of modules
+cvs -z3 -d:pserver:anonym...@thera-pi.cvs.sourceforge.net:/cvsroot/thera-pi co
-l -dtmpXXX .
+cd tmpXXX
+cvs -n update -d modules.list
+MODULES=` cat modules.list|awk '{print $5}'|\
+ sed s/_/Q/g|tr -d [:punct:]|sed s/Q/_/g`
+cd
[med-svn] r13430 - in trunk/packages/treeview/trunk: . debian debian/patches
Author: alteholz Date: 2013-04-27 10:13:44 + (Sat, 27 Apr 2013) New Revision: 13430 Removed: trunk/packages/treeview/trunk/README.status trunk/packages/treeview/trunk/debian/treeview.links Modified: trunk/packages/treeview/trunk/debian/README.Debian trunk/packages/treeview/trunk/debian/changelog trunk/packages/treeview/trunk/debian/copyright trunk/packages/treeview/trunk/debian/get-orig-source trunk/packages/treeview/trunk/debian/patches/classpath.patch trunk/packages/treeview/trunk/debian/rules trunk/packages/treeview/trunk/debian/treeview.docs Log: final version Deleted: trunk/packages/treeview/trunk/README.status === --- trunk/packages/treeview/trunk/README.status 2013-04-26 13:36:33 UTC (rev 13429) +++ trunk/packages/treeview/trunk/README.status 2013-04-27 10:13:44 UTC (rev 13430) @@ -1,6 +0,0 @@ -Format: 1 -Status: draft -Comment: - Work on this project was started by Steffen M�ller but has stalled. - Feel free to take it over. Modified: trunk/packages/treeview/trunk/debian/README.Debian === --- trunk/packages/treeview/trunk/debian/README.Debian 2013-04-26 13:36:33 UTC (rev 13429) +++ trunk/packages/treeview/trunk/debian/README.Debian 2013-04-27 10:13:44 UTC (rev 13430) @@ -1,6 +1,16 @@ treeview for Debian --- -I need help with the correct specification of the dependency to non-free Java 1.4. +The following files have been removed as it seems that +they are not needed for a Debian package: - -- Steffen Moeller moel...@pzr.uni-rostock.de, Wed, 7 Apr 2004 22:02:54 +0200 +# Debian version is used +lib/nanoxml-2.2.2.jar +# not needed for build +src/edu/stanford/genetics/treeview/plugin/dendroview/dendroview.jar +# only needed for os X +compile_lib/jarbundler-1.8.1.jar +compile_lib/xercesImpl.jar +compile_lib/xml-apis.jar +# only needed for windows +windows-installer.tar.gz Modified: trunk/packages/treeview/trunk/debian/changelog === --- trunk/packages/treeview/trunk/debian/changelog 2013-04-26 13:36:33 UTC (rev 13429) +++ trunk/packages/treeview/trunk/debian/changelog 2013-04-27 10:13:44 UTC (rev 13430) @@ -1,13 +1,6 @@ -treeview (1.1.6.2+dfsg-1) UNRELEASED; urgency=low +treeview (1.1.6.2+dfsg-1) unstable; urgency=low * Initial release (Closes: #243771) - * TODO: ITP #243771 has to be reopened in case of upload - * TODO: debian/upstream - * TODO: debian/copyright - * TODO: exception - * TODO: either package included JAR files separately from source - or list according licenses in debian/copyright (in the - latter case package needs to go to non-free [ Thorsten Alteholz ] * debian/watch: watch file added @@ -25,7 +18,7 @@ * debian/source/format: 3.0 (quilt) * Added myself to Uploaders - -- Thorsten Alteholz deb...@alteholz.de Mon, 23 Jan 2012 18:00:00 +0100 + -- Thorsten Alteholz deb...@alteholz.de Fri, 26 Apr 2013 18:00:00 +0200 treeview (1.0.5-0.3) UNRELEASED; urgency=low Modified: trunk/packages/treeview/trunk/debian/copyright === --- trunk/packages/treeview/trunk/debian/copyright 2013-04-26 13:36:33 UTC (rev 13429) +++ trunk/packages/treeview/trunk/debian/copyright 2013-04-27 10:13:44 UTC (rev 13430) @@ -3,8 +3,86 @@ Source: http://treeview.sourceforge.net/ Files: * -Copyright: Alok Saldanha a...@caltech.edu +Copyright: 2001-2003 Alok Saldanha a...@caltech.edu License: GPL-2 + +Files: src/LinkedView.java +Copyright: 2001-2003 Alok Saldanha a...@caltech.edu + 2013 Alex Segal, Lawrence Berkeley Lab +License: GPL-2 + +Files: src/edu/* +Copyright: 2001-2003 Alok Saldanha a...@caltech.edu + 2013 Alex Segal, Lawrence Berkeley Lab +License: GPL-2 + +Files: edu/stanford/genetics/treeview/NatField.java +Copyright: 1997 Rob Arthan, Lemma 1 Ltd. + 2001-2003 Alok Saldanha a...@caltech.edu + 2013 Alex Segal, Lawrence Berkeley Lab +License: GPL-2 + +Files: com/gurge/amd/Quantize.java +Copyright: 2000 Adam Doppelt, E. I. du Pont de Nemours and Company +License: ImageMagick + Permission is hereby granted, free of charge, to any person obtaining a + copy of this software and associated documentation files (ImageMagick), + to deal in ImageMagick without restriction, including without limitation + the rights to use, copy, modify, merge, publish, distribute, sublicense, + and/or sell copies of ImageMagick, and to permit persons to whom the + ImageMagick is furnished to do so, subject to the following conditions: + . + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of ImageMagick. + . + The software is provided as is, without warranty of any kind, express or + implied, including but not limited to the warranties
[med-svn] r13431 - trunk/packages/treeview/trunk/debian
Author: alteholz Date: 2013-04-27 10:17:02 + (Sat, 27 Apr 2013) New Revision: 13431 Added: trunk/packages/treeview/trunk/debian/upstream Log: upstream information Added: trunk/packages/treeview/trunk/debian/upstream === --- trunk/packages/treeview/trunk/debian/upstream (rev 0) +++ trunk/packages/treeview/trunk/debian/upstream 2013-04-27 10:17:02 UTC (rev 13431) @@ -0,0 +1,12 @@ +Reference: + Author: Alok J. Saldanha + Title: Java Treeview -- extensible visualization of microarray data + Journal: Bioinformatics + Year: 2004 + Volume: 20 + Number: 17 + Pages: 3246-3248 + DOI: 10.1093/bioinformatics/bth349 + PMID: 21653522 + URL: http://bioinformatics.oxfordjournals.org/content/20/17/3246.abstract + eprint: http://bioinformatics.oxfordjournals.org/content/20/17/3246.full.pdf+html ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13418 - in trunk/packages/treeview/trunk/debian: . patches
Author: alteholz
Date: 2013-04-25 19:28:45 + (Thu, 25 Apr 2013)
New Revision: 13418
Added:
trunk/packages/treeview/trunk/debian/treeview.doc-base.programmer-guide
trunk/packages/treeview/trunk/debian/treeview.doc-base.user-manual
trunk/packages/treeview/trunk/debian/treeview.docs
Modified:
trunk/packages/treeview/trunk/debian/changelog
trunk/packages/treeview/trunk/debian/control
trunk/packages/treeview/trunk/debian/get-orig-source
trunk/packages/treeview/trunk/debian/patches/classpath.patch
trunk/packages/treeview/trunk/debian/rules
trunk/packages/treeview/trunk/debian/treeview.install
trunk/packages/treeview/trunk/debian/treeview.links
Log:
working plugins, docu available, windows stuff eliminated
Modified: trunk/packages/treeview/trunk/debian/changelog
===
--- trunk/packages/treeview/trunk/debian/changelog 2013-04-25 13:01:16 UTC
(rev 13417)
+++ trunk/packages/treeview/trunk/debian/changelog 2013-04-25 19:28:45 UTC
(rev 13418)
@@ -2,9 +2,9 @@
* Initial release (Closes: #243771)
* TODO: ITP #243771 has to be reopened in case of upload
- * TODO: take care of plugins
- * TODO: remove windows stuff
- * TODO: build docu
+ * TODO: debian/upstream
+ * TODO: debian/copyright
+ * TODO: exception
* TODO: either package included JAR files separately from source
or list according licenses in debian/copyright (in the
latter case package needs to go to non-free
Modified: trunk/packages/treeview/trunk/debian/control
===
--- trunk/packages/treeview/trunk/debian/control2013-04-25 13:01:16 UTC
(rev 13417)
+++ trunk/packages/treeview/trunk/debian/control2013-04-25 19:28:45 UTC
(rev 13418)
@@ -10,7 +10,13 @@
default-jdk,
libnanoxml2-java,
libcommons-configuration-java,
- libcommons-lang-java
+ libcommons-lang-java,
+ libxerces2-java,
+ docbook-xsl,
+ docbook-to-man,
+ xsltproc,
+ fop,
+ libservlet3.0-java
Standards-Version: 3.9.4
Homepage: http://jtreeview.sourceforge.net
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/treeview/trunk/
Modified: trunk/packages/treeview/trunk/debian/get-orig-source
===
--- trunk/packages/treeview/trunk/debian/get-orig-source2013-04-25
13:01:16 UTC (rev 13417)
+++ trunk/packages/treeview/trunk/debian/get-orig-source2013-04-25
19:28:45 UTC (rev 13418)
@@ -32,6 +32,12 @@
# we do not need windows stuff here
rm windows-installer.tar.gz
rm lib/nanoxml-2.2.2.jar
+# these jars are only needed for mac osx
+#XXX rm compile_lib/jarbundler-1.8.1.jar
+rm compile_lib/xercesImpl.jar
+rm compile_lib/xml-apis.jar
+#ln -s /usr/share/java/xml-apis.jar compile_lib/xml-apis.jar
+#ln -s /usr/share/java/xercesImpl.jar compile_lib/xercesImpl.jar
cd ..
rm $UTAR
Modified: trunk/packages/treeview/trunk/debian/patches/classpath.patch
===
--- trunk/packages/treeview/trunk/debian/patches/classpath.patch
2013-04-25 13:01:16 UTC (rev 13417)
+++ trunk/packages/treeview/trunk/debian/patches/classpath.patch
2013-04-25 19:28:45 UTC (rev 13418)
@@ -1,10 +1,20 @@
Description: do not use internal lib
Author: Thorsten Alteholz deb...@alteholz.de
-Index: TreeView-1.1.6r2-src/build.xml
+Index: treeview_1.1.6.2+dfsg.orig/build.xml
===
TreeView-1.1.6r2-src.orig/build.xml2013-04-22 13:11:09.0
+0200
-+++ TreeView-1.1.6r2-src/build.xml 2013-04-22 13:16:03.0 +0200
-@@ -211,7 +211,7 @@
+--- treeview_1.1.6.2+dfsg.orig.orig/build.xml 2013-04-25 13:25:43.0
+0200
treeview_1.1.6.2+dfsg.orig/build.xml 2013-04-25 13:44:05.0
+0200
+@@ -83,6 +83,9 @@
+ fileset dir=${app.libs}
+ include name=*.jar/
+ /fileset
++ fileset dir=/usr/share/java
++ include name=nanoxml.jar /
++ /fileset
+ fileset dir=${compile.lib}
+ include name=*.jar/
+ /fileset
+@@ -211,7 +214,7 @@
excludes=edu/stanford/genetics/treeview/plugin/**
manifest
attribute name=Main-Class value=LinkedView/
@@ -13,7 +23,7 @@
/manifest
/jar
-@@ -226,7 +226,7 @@
+@@ -226,7 +229,7 @@
excludes=*coordinates/*,edu/stanford/genetics/treeview/plugin/**,edu/stanford/genetics/treeview/reg/**
manifest
attribute name=Main-Class value=LinkedView/
@@ -22,24 +32,21 @@
/manifest
/jar
/target
-@@ -241,9 +241,11 @@
- copy todir=applet
+@@ -242,7 +245,7 @@
fileset dir=appletStatic/
/copy
-+!-- not needed anymore (XXX)
copy todir=applet
- fileset file=lib/nanoxml-2.2.2.jar/
+- fileset file=lib/nanoxml-2.2.2.jar
[med-svn] r13380 - in trunk/packages/treeview/trunk/debian: . patches scripts
Author: alteholz
Date: 2013-04-22 19:57:07 + (Mon, 22 Apr 2013)
New Revision: 13380
Added:
trunk/packages/treeview/trunk/debian/get-orig-source
trunk/packages/treeview/trunk/debian/patches/
trunk/packages/treeview/trunk/debian/patches/classpath.patch
trunk/packages/treeview/trunk/debian/patches/series
trunk/packages/treeview/trunk/debian/scripts/
trunk/packages/treeview/trunk/debian/scripts/treeview
trunk/packages/treeview/trunk/debian/treeview.install
trunk/packages/treeview/trunk/debian/treeview.links
trunk/packages/treeview/trunk/debian/treeview.manpages
Removed:
trunk/packages/treeview/trunk/debian/treeview
Modified:
trunk/packages/treeview/trunk/debian/changelog
trunk/packages/treeview/trunk/debian/compat
trunk/packages/treeview/trunk/debian/control
trunk/packages/treeview/trunk/debian/copyright
trunk/packages/treeview/trunk/debian/menu
trunk/packages/treeview/trunk/debian/rules
trunk/packages/treeview/trunk/debian/watch
Log:
some progress, not ready yet
Modified: trunk/packages/treeview/trunk/debian/changelog
===
--- trunk/packages/treeview/trunk/debian/changelog 2013-04-22 14:17:41 UTC
(rev 13379)
+++ trunk/packages/treeview/trunk/debian/changelog 2013-04-22 19:57:07 UTC
(rev 13380)
@@ -1,8 +1,10 @@
-treeview (1.1.6.2-1) UNRELEASED; urgency=low
+treeview (1.1.6.2+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #243771)
-TODO: ITP #243771 has to be reopened in case of upload
- * TODO: remove lintian complaints
+ * TODO: ITP #243771 has to be reopened in case of upload
+ * TODO: take care of plugins
+ * TODO: remove windows stuff
+ * TODO: build docu
* TODO: either package included JAR files separately from source
or list according licenses in debian/copyright (in the
latter case package needs to go to non-free
@@ -10,8 +12,8 @@
[ Thorsten Alteholz ]
* debian/watch: watch file added
* debian/rules: target get-orig-source added
- * debian/control: debhelper 8
- * debian/control: standards version 3.9.2 (no other changes)
+ * debian/control: debhelper 9
+ * debian/control: standards version 3.9.4 (no other changes)
* debian/control: vcs fields added
* debian/control: team maintenance
* new upstream release: 1.1.6.2
@@ -23,7 +25,7 @@
* debian/source/format: 3.0 (quilt)
* Added myself to Uploaders
- -- DMPT debian-med-packag...@lists.alioth.debian.org Mon, 23 Jan 2012
18:00:00 +0100
+ -- Thorsten Alteholz deb...@alteholz.de Mon, 23 Jan 2012 18:00:00 +0100
treeview (1.0.5-0.3) UNRELEASED; urgency=low
Modified: trunk/packages/treeview/trunk/debian/compat
===
--- trunk/packages/treeview/trunk/debian/compat 2013-04-22 14:17:41 UTC (rev
13379)
+++ trunk/packages/treeview/trunk/debian/compat 2013-04-22 19:57:07 UTC (rev
13380)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/treeview/trunk/debian/control
===
--- trunk/packages/treeview/trunk/debian/control2013-04-22 14:17:41 UTC
(rev 13379)
+++ trunk/packages/treeview/trunk/debian/control2013-04-22 19:57:07 UTC
(rev 13380)
@@ -3,16 +3,26 @@
Priority: optional
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Uploaders: Steffen Moeller moel...@debian.org,
- Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 8), ant, java2-compiler
-Standards-Version: 3.9.2
+ Andreas Tille ti...@debian.org,
+ Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9),
+ ant,
+ default-jdk,
+ libnanoxml2-java,
+ libcommons-configuration-java,
+ libcommons-lang-java
+Standards-Version: 3.9.4
Homepage: http://jtreeview.sourceforge.net
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/treeview/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/treeview/trunk/
Package: treeview
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, java2-runtime
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ default-jre,
+ libnanoxml2-java,
+ libcommons-configuration-java,
+ libcommons-lang-java
Recommends: cluster3
Suggests: mapletree, smile
Description: Java re-implementation of Michael Eisen's TreeView
Modified: trunk/packages/treeview/trunk/debian/copyright
===
--- trunk/packages/treeview/trunk/debian/copyright 2013-04-22 14:17:41 UTC
(rev 13379)
+++ trunk/packages/treeview/trunk/debian/copyright 2013-04-22 19:57:07 UTC
(rev 13380)
@@ -1,26 +1,30 @@
-This package was debianized by Steffen Moeller moel...@pzr.uni-rostock.de on
-Wed, 7 Apr 2004 22:02:54 +0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: treeview
+Source: http://treeview.sourceforge.net/
-It was downloaded from http://treeview.sourceforge.net
[med-svn] r13381 - trunk/packages/qrisk2/trunk/debian
Author: alteholz Date: 2013-04-22 19:58:32 + (Mon, 22 Apr 2013) New Revision: 13381 Modified: trunk/packages/qrisk2/trunk/debian/changelog trunk/packages/qrisk2/trunk/debian/control Log: remove needless . at end of long description Modified: trunk/packages/qrisk2/trunk/debian/changelog === --- trunk/packages/qrisk2/trunk/debian/changelog2013-04-22 19:57:07 UTC (rev 13380) +++ trunk/packages/qrisk2/trunk/debian/changelog2013-04-22 19:58:32 UTC (rev 13381) @@ -1,3 +1,9 @@ +qrisk2 (0.0.r30-2) UNRELEASED; urgency=low + + * debian/control: remove . at end of long description (Closes: #705791) + + -- Thorsten Alteholz deb...@alteholz.de Mon, 22 Apr 2013 18:00:00 +0200 + qrisk2 (0.0.r30-1) unstable; urgency=low * Initial release (Closes: #705694) @@ -4,4 +10,3 @@ Part of packaging has been done by Andreas Tille -- Thorsten Alteholz deb...@alteholz.de Thu, 18 Apr 2013 18:00:00 +0200 - Modified: trunk/packages/qrisk2/trunk/debian/control === --- trunk/packages/qrisk2/trunk/debian/control 2013-04-22 19:57:07 UTC (rev 13380) +++ trunk/packages/qrisk2/trunk/debian/control 2013-04-22 19:58:32 UTC (rev 13381) @@ -32,4 +32,4 @@ deprived areas and over-estimated for patients from affluent areas. All medical decisions need to be taken by a patient in consultation with their doctor. The authors and the sponsors accept no responsibility for - clinical use or misuse of these score.. + clinical use or misuse of these score. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13358 - trunk/packages/visionegg/trunk/debian
Author: alteholz Date: 2013-04-20 17:09:25 + (Sat, 20 Apr 2013) New Revision: 13358 Modified: trunk/packages/visionegg/trunk/debian/upstream Log: typo Modified: trunk/packages/visionegg/trunk/debian/upstream === --- trunk/packages/visionegg/trunk/debian/upstream 2013-04-20 17:07:13 UTC (rev 13357) +++ trunk/packages/visionegg/trunk/debian/upstream 2013-04-20 17:09:25 UTC (rev 13358) @@ -1,5 +1,5 @@ Reference: - Author: Andrew D. aw + Author: Andrew D. Straw Title: Vision Egg: An Open-Source Library for Realtime Visual Stimulus Generation Journal: Frontiers in Neuroinformatics Year: 2008 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13349 - in trunk/packages/qrisk2/trunk/debian: . patches source
/Q68_qrisk2_2012_1_1_commandLine.1 (rev 0) +++ trunk/packages/qrisk2/trunk/debian/Q68_qrisk2_2012_1_1_commandLine.1 2013-04-18 17:36:11 UTC (rev 13349) @@ -0,0 +1,65 @@ +.\ DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.2. +.TH Q68_QRISK2_2012_1_1_COMMANDLINE 1 April 2013 Q68_qrisk2_2012_1_1_commandLine * Copyright 2012 ClinRisk Ltd. User Commands +.SH NAME +Q68_qrisk2_2012_1_1_commandLine \- male version of 2012 risk analysis +.SS Usage: +.IP +Q68_qrisk2_2012_1_1_commandLine age b_AF b_ra b_renal b_treatedhyp b_type2 bmi ethrisk fh_cvd rati sbp smoke_cat surv town +.TP +\fBage\fR age of person (30..84) +.TP +\fBb_AF\fR Atrial fibrillation (0..1) +.TP +\fBb_ra\fR Rheumatoid arthritis (0..1) +.TP +\fBb_renal\fR +.TP +\fBb_treatedhyp\fR On blood pressure treatment (0..1) +.TP +\fBb_type2\fR Diabetic (0..1) +.TP +\fBbmi\fR Body Mass Index (20..40) +.TP +\fBethrisk\fR Ethnicity +.IP +\fB1\fR white or not stated +.IP +\fB2\fR Indian +.IP +\fB3\fR Pakistani +.IP +\fB4\fR Bangladeshi +.IP +\fB5\fR Other Asian +.IP +\fB6\fR Black Caribbean +.IP +\fB7\fR Black African +.IP +\fB8\fR Chinese +.IP +\fB9\fR Other ethnic group +.TP +\fBfh_cvd\fR +.TP +\fBrati\fR Cholesterol/HDL ratio (1..12) +.TP +\fBsbp\fR Systolic blood pressure (mmHg) (70..210) +.TP +\fBsmoke_cat\fR Smoking status (0..4) +.IP +\fB0\fR non smoker +.IP +\fB1\fR ex smoker +.IP +\fB2\fR light smoker (10) +.IP +\fB3\fR moderate smoker (10..19) +.IP +\fB4\fR heavy smoker =20 +.TP +\fBsurv\fR +.TP +\fBtown\fR UK postcode + +.IP Added: trunk/packages/qrisk2/trunk/debian/Q68_qrisk2_2012_1_1_qriskAge.1 === --- trunk/packages/qrisk2/trunk/debian/Q68_qrisk2_2012_1_1_qriskAge.1 (rev 0) +++ trunk/packages/qrisk2/trunk/debian/Q68_qrisk2_2012_1_1_qriskAge.1 2013-04-18 17:36:11 UTC (rev 13349) @@ -0,0 +1,65 @@ +.\ DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.2. +.TH Q68_QRISK2_2012_1_1_QRISKAGE 1 April 2013 Q68_qrisk2_2012_1_1_qriskAge * Copyright 2012 ClinRisk Ltd. User Commands +.SH NAME +Q68_qrisk2_2012_1_1_qriskAge \- male version of 2012 risk age +.SS Usage: +.IP +Q68_qrisk2_2012_1_1_qriskAge age b_AF b_ra b_renal b_treatedhyp b_type2 bmi ethrisk fh_cvd rati sbp smoke_cat surv town +.TP +\fBage\fR age of person (30..84) +.TP +\fBb_AF\fR Atrial fibrillation (0..1) +.TP +\fBb_ra\fR Rheumatoid arthritis (0..1) +.TP +\fBb_renal\fR +.TP +\fBb_treatedhyp\fR On blood pressure treatment (0..1) +.TP +\fBb_type2\fR Diabetic (0..1) +.TP +\fBbmi\fR Body Mass Index (20..40) +.TP +\fBethrisk\fR Ethnicity +.IP +\fB1\fR white or not stated +.IP +\fB2\fR Indian +.IP +\fB3\fR Pakistani +.IP +\fB4\fR Bangladeshi +.IP +\fB5\fR Other Asian +.IP +\fB6\fR Black Caribbean +.IP +\fB7\fR Black African +.IP +\fB8\fR Chinese +.IP +\fB9\fR Other ethnic group +.TP +\fBfh_cvd\fR +.TP +\fBrati\fR Cholesterol/HDL ratio (1..12) +.TP +\fBsbp\fR Systolic blood pressure (mmHg) (70..210) +.TP +\fBsmoke_cat\fR Smoking status (0..4) +.IP +\fB0\fR non smoker +.IP +\fB1\fR ex smoker +.IP +\fB2\fR light smoker (10) +.IP +\fB3\fR moderate smoker (10..19) +.IP +\fB4\fR heavy smoker =20 +.TP +\fBsurv\fR +.TP +\fBtown\fR UK postcode + +.IP Modified: trunk/packages/qrisk2/trunk/debian/changelog === --- trunk/packages/qrisk2/trunk/debian/changelog2013-04-18 09:56:32 UTC (rev 13348) +++ trunk/packages/qrisk2/trunk/debian/changelog2013-04-18 17:36:11 UTC (rev 13349) @@ -1,5 +1,7 @@ -qrisk2 (0.0.r27-1) unstable; urgency=low +qrisk2 (0.0.r30-1) unstable; urgency=low - * Initial release + * Initial release (Closes: #705694) +Part of packaging has been done by Andreas Tille - -- Andreas Tille ti...@debian.org Thu, 07 Jun 2012 13:16:01 +0200 + -- Thorsten Alteholz deb...@alteholz.de Thu, 18 Apr 2013 18:00:00 +0200 + Modified: trunk/packages/qrisk2/trunk/debian/control === --- trunk/packages/qrisk2/trunk/debian/control 2013-04-18 09:56:32 UTC (rev 13348) +++ trunk/packages/qrisk2/trunk/debian/control 2013-04-18 17:36:11 UTC (rev 13349) @@ -2,10 +2,11 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes -Uploaders: Andreas Tille ti...@debian.org -Build-Depends: debhelper (= 9) -Standards-Version: 3.9.3 +Uploaders: Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de +Build-Depends: debhelper (= 9), + xutils-dev +Standards-Version: 3.9.4 Homepage: http://qrisk.org/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qrisk2/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qrisk2/trunk/ Modified: trunk/packages/qrisk2/trunk/debian/copyright === --- trunk/packages/qrisk2/trunk/debian/copyright2013-04
[med-svn] r13324 - in trunk/packages: . visionegg visionegg/trunk visionegg/trunk/debian visionegg/trunk/debian/source
Author: alteholz
Date: 2013-04-16 17:24:17 + (Tue, 16 Apr 2013)
New Revision: 13324
Added:
trunk/packages/visionegg/
trunk/packages/visionegg/trunk/
trunk/packages/visionegg/trunk/debian/
trunk/packages/visionegg/trunk/debian/changelog
trunk/packages/visionegg/trunk/debian/compat
trunk/packages/visionegg/trunk/debian/control
trunk/packages/visionegg/trunk/debian/copyright
trunk/packages/visionegg/trunk/debian/python-visionegg.install
trunk/packages/visionegg/trunk/debian/rules
trunk/packages/visionegg/trunk/debian/source/
trunk/packages/visionegg/trunk/debian/source/format
trunk/packages/visionegg/trunk/debian/watch
Log:
initial version of visionegg
Property changes on: trunk/packages/visionegg/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/visionegg/trunk/debian/changelog
===
--- trunk/packages/visionegg/trunk/debian/changelog
(rev 0)
+++ trunk/packages/visionegg/trunk/debian/changelog 2013-04-16 17:24:17 UTC
(rev 13324)
@@ -0,0 +1,6 @@
+visionegg (1.2.1-1) unstable; urgency=low
+
+ * initial version (Closes: #365856)
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 16 Apr 2013 18:00:07 +0200
+
Added: trunk/packages/visionegg/trunk/debian/compat
===
--- trunk/packages/visionegg/trunk/debian/compat
(rev 0)
+++ trunk/packages/visionegg/trunk/debian/compat2013-04-16 17:24:17 UTC
(rev 13324)
@@ -0,0 +1 @@
+9
Added: trunk/packages/visionegg/trunk/debian/control
===
--- trunk/packages/visionegg/trunk/debian/control
(rev 0)
+++ trunk/packages/visionegg/trunk/debian/control 2013-04-16 17:24:17 UTC
(rev 13324)
@@ -0,0 +1,26 @@
+Source: visionegg
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9),
+ python-all-dev (=2.6),
+ python-setuptools,
+ python-numpy,
+ python-imaging,
+ python-opengl,
+ python-pygame,
+ mesa-common-dev,
+ libgl1-mesa-dev
+Standards-Version: 3.9.4
+Homepage: http://www.visionegg.org
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/visionegg/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/visionegg/trunk/
+
+Package: python-visionegg
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libgl1-mesa-glx
+Description: Python library for 2D/3D visual stimulus generation
+ The Vision Egg is a programming library that uses standard, inexpensive
+ computer graphics cards to produce visual stimuli for vision research
+ experiments.
Added: trunk/packages/visionegg/trunk/debian/copyright
===
--- trunk/packages/visionegg/trunk/debian/copyright
(rev 0)
+++ trunk/packages/visionegg/trunk/debian/copyright 2013-04-16 17:24:17 UTC
(rev 13324)
@@ -0,0 +1,85 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: visionegg
+Source: http://www.visionegg.org
+
+Files: *
+Copyright: 2001-2003 Andrew Straw
+ 2004-2008 California Institute of Technology
+License: LGPL 2.1
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2.1 can be found in
/usr/share/common-licenses/LGPL-2.
+
+Files: VisionEgg/DaqKeyboard.py
+ VisionEgg/ResponseControl.py
+ demo/demo_fixationpoint.py
+ demo/demo_keyboardresponse.py
+ demo/demo_keyboardtrigger.py
+Copyright: 2005 Hubertus Becker, Hertie Institute for Clinical Brain Research,
+ Department of Cognitive Neurology, University of Tuebingen
+License: LGPL 2.1
+ see above
+
+Files: VisoinEgg/MoreStimuli.py
+Copyright: 2001-2003 Andrew Straw.
+ 2005 by Hertie Institute for Clinical Brain Research,
+Department of Cognitive Neurology, University of Tuebingen
[med-svn] r13311 - trunk/packages/bagpipe/trunk/debian
Author: alteholz
Date: 2013-04-13 15:38:56 + (Sat, 13 Apr 2013)
New Revision: 13311
Modified:
trunk/packages/bagpipe/trunk/debian/control
Log:
need R package
Modified: trunk/packages/bagpipe/trunk/debian/control
===
--- trunk/packages/bagpipe/trunk/debian/control 2013-04-13 04:43:30 UTC (rev
13310)
+++ trunk/packages/bagpipe/trunk/debian/control 2013-04-13 15:38:56 UTC (rev
13311)
@@ -11,7 +11,7 @@
Package: bagpipe
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends},
r-other-valdar-bagpipe.backend
Description: genomewide LD mapping
Bagpipe is a program for performing genomewide linkage disequilibrium
mapping of quantitative trait loci in populations whose genome structure
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13312 - in trunk/packages/R: . r-other-valdar-bagpipe.backend r-other-valdar-bagpipe.backend/trunk r-other-valdar-bagpipe.backend/trunk/debian r-other-valdar-bagpipe.backend/trunk/debian/so
Author: alteholz
Date: 2013-04-13 15:48:17 + (Sat, 13 Apr 2013)
New Revision: 13312
Added:
trunk/packages/R/r-other-valdar-bagpipe.backend/
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/changelog
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/compat
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/control
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/rules
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/source/
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/source/format
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/watch
Log:
R package for bagpipe (just the beginning)
Property changes on:
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/changelog
===
--- trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/changelog
(rev 0)
+++ trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/changelog
2013-04-13 15:48:17 UTC (rev 13312)
@@ -0,0 +1,8 @@
+bagpipe.backend (0.28-1) UNRELEASED; urgency=low
+
+ * TODO this package is needed for package bagpipe,
+ but waiting for at least version 3 of r-cran-evd (but take it easy!!)
+ * initial version (Closes: #XX)
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 09 Apr 2013 18:00:07 +0200
+
Added: trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/compat
===
--- trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/compat
(rev 0)
+++ trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/compat
2013-04-13 15:48:17 UTC (rev 13312)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/control
===
--- trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/control
(rev 0)
+++ trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/control
2013-04-13 15:48:17 UTC (rev 13312)
@@ -0,0 +1,34 @@
+Source: bagpipe.backend
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9.0.0),
+ r-base-dev,
+ r-cran-evd,
+ r-cran-bitops,
+ dpkg-dev (= 1.16.1~)
+Standards-Version: 3.9.4
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-valdar-bagpipe/trunk/
+Vcs-Svn:
svn://svn.debian.org/debian-med/trunk/packages/R/r-other-valdar-bagpipe/trunk/
+Homepage: http://www.omegahat.org/RCurl/XXX
+
+Package: r-other-valdar-bagpipe.backend
+Architecture: any
+Depends: ${shlibs:Depends}, ${R-Depends}, ${misc:Depends}
+Suggests: r-cran-xml,r-cran-rcompression
+Provides: r-omegahat-rcurl, r-bioc-rcurl
+Description: GNU R package for network access
+ The package allows one to compose general HTTP requests and provides
+ convenient functions to fetch URIs, get post forms, etc. and process
+ the results returned by the Web server. This provides a great deal of
+ control over the HTTP/FTP/... connection and the form of the request
+ while providing a higher-level interface than is available just using
+ R socket connections. Additionally, the underlying implementation is
+ robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads),
+ SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects,
+ authentication, etc.
+ .
+ The package has its origin at omegahat.org and it is also found at
+ bioconductor.org.
+
Added: trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/rules
===
--- trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/rules
(rev 0)
+++ trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/rules
2013-04-13 15:48:17 UTC (rev 13312)
@@ -0,0 +1,10 @@
+#!/usr/bin/make -f
+
+debRreposname=other-valdar
+
+include /usr/share/R/debian/r-cran.mk
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
+
Property changes on:
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/rules
___
Added: svn:executable
+ *
Added:
trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/source/format
===
--- trunk/packages/R/r-other-valdar-bagpipe.backend/trunk/debian/source/format
[med-svn] r13279 - trunk/packages/bagphenotype/trunk
Author: alteholz Date: 2013-04-09 17:51:55 + (Tue, 09 Apr 2013) New Revision: 13279 Removed: trunk/packages/bagphenotype/trunk/debian/ Log: upstream sources not available anymore, better use bagpipe ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13280 - trunk/packages/bagphenotype/trunk
Author: alteholz Date: 2013-04-09 17:52:31 + (Tue, 09 Apr 2013) New Revision: 13280 Added: trunk/packages/bagphenotype/trunk/README.status Log: upstream sources not available anymore, better use bagpipe Added: trunk/packages/bagphenotype/trunk/README.status === --- trunk/packages/bagphenotype/trunk/README.status (rev 0) +++ trunk/packages/bagphenotype/trunk/README.status 2013-04-09 17:52:31 UTC (rev 13280) @@ -0,0 +1,13 @@ +--- +Format: 1 +Status: removed +SVNDeleteRevision: 13279 +Comment: + bagphenotype packaging was removed because there is a successor for it, + which is called bagpipe. + Meanwhile even the source code is no longer available on the Valdarlab + website: http://valdarlab.unc.edu/bagphenotype.html + . + Feel free to continue with packaging at + svn://svn.debian.org/debian-med/trunk/packages/bagpipe/trunk/ + if you are interested. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13281 - trunk/packages/bagphenotype
Author: alteholz Date: 2013-04-09 17:53:13 + (Tue, 09 Apr 2013) New Revision: 13281 Removed: trunk/packages/bagphenotype/README trunk/packages/bagphenotype/r-other-valdar-bagphenotype Log: upstream sources not available anymore, better use bagpipe Deleted: trunk/packages/bagphenotype/README === --- trunk/packages/bagphenotype/README 2013-04-09 17:52:31 UTC (rev 13280) +++ trunk/packages/bagphenotype/README 2013-04-09 17:53:13 UTC (rev 13281) @@ -1,2 +0,0 @@ -bagphenotype - the perl code primarily used -r-other-valdar-bagphenotype- the R code that the perl code uses Deleted: trunk/packages/bagphenotype/r-other-valdar-bagphenotype === --- trunk/packages/bagphenotype/r-other-valdar-bagphenotype 2013-04-09 17:52:31 UTC (rev 13280) +++ trunk/packages/bagphenotype/r-other-valdar-bagphenotype 2013-04-09 17:53:13 UTC (rev 13281) @@ -1 +0,0 @@ -link ../R/r-other-valdar-bagphenotype/ \ No newline at end of file ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13282 - in trunk/packages: . bagpipe bagpipe/trunk bagpipe/trunk/debian bagpipe/trunk/debian/script bagpipe/trunk/debian/source
+example_config
+\- Write an example config file to config.example
+.SS Web
+.TP
+More information can be found at:
+http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html
Added: trunk/packages/bagpipe/trunk/debian/bagpipe.install
===
--- trunk/packages/bagpipe/trunk/debian/bagpipe.install
(rev 0)
+++ trunk/packages/bagpipe/trunk/debian/bagpipe.install 2013-04-09 17:54:02 UTC
(rev 13282)
@@ -0,0 +1,3 @@
+debian/script/bagpipe usr/bin
+bagpipe/bagpipe.pl usr/share/bagpipe
+bagpipe/lib/* usr/share/perl5/Bagpipe
Added: trunk/packages/bagpipe/trunk/debian/bagpipe.manpages
===
--- trunk/packages/bagpipe/trunk/debian/bagpipe.manpages
(rev 0)
+++ trunk/packages/bagpipe/trunk/debian/bagpipe.manpages2013-04-09
17:54:02 UTC (rev 13282)
@@ -0,0 +1 @@
+debian/bagpipe.1
Added: trunk/packages/bagpipe/trunk/debian/changelog
===
--- trunk/packages/bagpipe/trunk/debian/changelog
(rev 0)
+++ trunk/packages/bagpipe/trunk/debian/changelog 2013-04-09 17:54:02 UTC
(rev 13282)
@@ -0,0 +1,6 @@
+bagpipe (2012.02.15-1) UNRELEASED; urgency=low
+
+ * initial version (Closes: #XX)
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 09 Apr 2013 18:00:07 +0200
+
Added: trunk/packages/bagpipe/trunk/debian/compat
===
--- trunk/packages/bagpipe/trunk/debian/compat (rev 0)
+++ trunk/packages/bagpipe/trunk/debian/compat 2013-04-09 17:54:02 UTC (rev
13282)
@@ -0,0 +1 @@
+9
Added: trunk/packages/bagpipe/trunk/debian/control
===
--- trunk/packages/bagpipe/trunk/debian/control (rev 0)
+++ trunk/packages/bagpipe/trunk/debian/control 2013-04-09 17:54:02 UTC (rev
13282)
@@ -0,0 +1,45 @@
+Source: bagpipe
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9)
+Standards-Version: 3.9.4
+Homepage: http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/bagpipe/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagpipe/trunk/
+
+Package: bagpipe
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Description: genomewide LD mapping
+ Bagpipe is a program for performing genomewide linkage disequilibrium
+ mapping of quantitative trait loci in populations whose genome structure
+ can be accommodated in the HAPPY framework [Mott00]. This includes most
+ diploid crosses where the founders of the individuals have known genotypes.
+ .
+ * Bagpipe is a simplified and streamlined version of Bagphenotype that
+does not currently include resample model averaging (RMA) capabilities.
+ * Bagpipe can help fit single locus regression models (with or without
+random effects) to marker intervals whose genetic ancestry is inferred
+using the HAPPY software.
+ * Bagpipe cannot help you decide what is a sensible model to fit.
+ * Bagpipe does not currently accommodate populations with significant
+population structure, except through the specification of simple random
+intercepts based on unpatterned covariance matrices.
+ * Bagpipe is named after the Scottish wind instrument the bagpipes and
+after Bagphenotype, which in turn was a PIPEline for BAGging-based
+multiple QTL analysis of phenoTYPEs. Bagphenotype was in turn based
+on software written by Richard Mott and William Valdar to analyze
+heterogeneous stock mice in [Valdar06].
+ * Bagpipe is experimental software, is provided free of charge subject to
+copyleft restrictions, and comes with no guarantees whatsoever.
+ .
+ [Mott00] Mott R, Talbot CJ, Turri MG, Collins AC, Flint, J (2000)
+ A method for fine mapping quantitative trait loci in outbred animal
+ stocks. Proceedings of the National Academy of Sciences of the United
+ States of America, 97(23), 12649-54.
+ [Valdar06] Valdar W, Solberg LC, Gaugier D, Burnett S, Klenerman P,
+ Cookson WO, Taylor M, Rawlins JNP, Mott R, Flint J (2006)
+ Genome-wide genetic association of complex traits in outbred mice.
+ Nature Genetics 38(8):879-87. PMID:16832355
Added: trunk/packages/bagpipe/trunk/debian/copyright
===
--- trunk/packages/bagpipe/trunk/debian/copyright
(rev 0)
+++ trunk/packages/bagpipe/trunk/debian/copyright 2013-04-09 17:54:02 UTC
(rev 13282)
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals
[med-svn] r13270 - in trunk/packages: . python-clips python-clips/trunk python-clips/trunk/debian python-clips/trunk/debian/source
Author: alteholz
Date: 2013-04-08 17:20:56 + (Mon, 08 Apr 2013)
New Revision: 13270
Added:
trunk/packages/python-clips/
trunk/packages/python-clips/trunk/
trunk/packages/python-clips/trunk/debian/
trunk/packages/python-clips/trunk/debian/changelog
trunk/packages/python-clips/trunk/debian/compat
trunk/packages/python-clips/trunk/debian/control
trunk/packages/python-clips/trunk/debian/copyright
trunk/packages/python-clips/trunk/debian/get-orig-source
trunk/packages/python-clips/trunk/debian/rules
trunk/packages/python-clips/trunk/debian/source/
trunk/packages/python-clips/trunk/debian/source/format
trunk/packages/python-clips/trunk/debian/watch
Log:
initial version of python-clips
Property changes on: trunk/packages/python-clips/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/python-clips/trunk/debian/changelog
===
--- trunk/packages/python-clips/trunk/debian/changelog
(rev 0)
+++ trunk/packages/python-clips/trunk/debian/changelog 2013-04-08 17:20:56 UTC
(rev 13270)
@@ -0,0 +1,6 @@
+python-clips (1.0.7.348+clips-1) unstable; urgency=low
+
+ * initial version (Closes: #577406)
+
+ -- Thorsten Alteholz deb...@alteholz.de Mon, 08 Apr 2013 18:00:07 +0100
+
Added: trunk/packages/python-clips/trunk/debian/compat
===
--- trunk/packages/python-clips/trunk/debian/compat
(rev 0)
+++ trunk/packages/python-clips/trunk/debian/compat 2013-04-08 17:20:56 UTC
(rev 13270)
@@ -0,0 +1 @@
+9
Added: trunk/packages/python-clips/trunk/debian/control
===
--- trunk/packages/python-clips/trunk/debian/control
(rev 0)
+++ trunk/packages/python-clips/trunk/debian/control2013-04-08 17:20:56 UTC
(rev 13270)
@@ -0,0 +1,21 @@
+Source: python-clips
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9),
+ python-all-dev
+Standards-Version: 3.9.4
+Homepage: http://sourceforge.net/projects/pyclips/
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/python-clips/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-clips/trunk/
+
+Package: python-clips
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Provides: ${python:Provides}
+Description: Python module to interface the CLIPS expert system shell library
+ CLIPS is an expert system shell / inference engine written by NASA
+ (see Debian package clips).
+ .
+ pyclips are the Python bindings to that engine.
Added: trunk/packages/python-clips/trunk/debian/copyright
===
--- trunk/packages/python-clips/trunk/debian/copyright
(rev 0)
+++ trunk/packages/python-clips/trunk/debian/copyright 2013-04-08 17:20:56 UTC
(rev 13270)
@@ -0,0 +1,64 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pyclips
+Source: http://sourceforge.net/projects/pyclips/
+
+Files: *
+Copyright: 2002-2008 Francesco Garosi/JKS
+License: LGPL-2
+
+Files: CLIPSSrc.zip
+Copyright: 2006 Barry Cameron, Bebe Ly, Brian L. Donnell,
+Chris Culbert, Gary D. Riley
+License: CLIPS
+
+Files: debian/*
+Copyright: 2013 Thorsten Alteholz deb...@alteholz.de
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see http://www.gnu.org/licenses/
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in /usr/share/common-licenses/GPL-2.
+
+License: LGPL-2
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2.1 can be found in
/usr/share/common-licenses/LGPL-2.
+
+License: CLIPS
+ CLIPS License Information
+ .
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the Software),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, and/or sell
[med-svn] r13271 - trunk/packages/uc-echo/trunk/debian
Author: alteholz Date: 2013-04-08 17:40:13 + (Mon, 08 Apr 2013) New Revision: 13271 Added: trunk/packages/uc-echo/trunk/debian/upstream Log: add some reference information Added: trunk/packages/uc-echo/trunk/debian/upstream === --- trunk/packages/uc-echo/trunk/debian/upstream (rev 0) +++ trunk/packages/uc-echo/trunk/debian/upstream2013-04-08 17:40:13 UTC (rev 13271) @@ -0,0 +1,9 @@ +Reference: + Author: W.-C. Kao and A.H. Chan and Y.S. Song + Title: ECHO: A reference-free short-read error correction algorithm + Journal: Genome Research + Year: 2011 + Volume: 21 + Pages: 1181--1192 + DOI: 10.1101/gr.111351.110 + PMID: PMC3129260 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13269 - in trunk/packages: . uc-echo uc-echo/trunk uc-echo/trunk/debian uc-echo/trunk/debian/patches uc-echo/trunk/debian/script uc-echo/trunk/debian/source
Author: alteholz
Date: 2013-04-07 14:33:19 + (Sun, 07 Apr 2013)
New Revision: 13269
Added:
trunk/packages/uc-echo/
trunk/packages/uc-echo/trunk/
trunk/packages/uc-echo/trunk/debian/
trunk/packages/uc-echo/trunk/debian/changelog
trunk/packages/uc-echo/trunk/debian/compat
trunk/packages/uc-echo/trunk/debian/control
trunk/packages/uc-echo/trunk/debian/copyright
trunk/packages/uc-echo/trunk/debian/patches/
trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch
trunk/packages/uc-echo/trunk/debian/patches/include.patch
trunk/packages/uc-echo/trunk/debian/patches/series
trunk/packages/uc-echo/trunk/debian/rules
trunk/packages/uc-echo/trunk/debian/script/
trunk/packages/uc-echo/trunk/debian/script/uc-echo
trunk/packages/uc-echo/trunk/debian/source/
trunk/packages/uc-echo/trunk/debian/source/format
trunk/packages/uc-echo/trunk/debian/uc-echo.1
trunk/packages/uc-echo/trunk/debian/uc-echo.install
trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides
trunk/packages/uc-echo/trunk/debian/uc-echo.manpages
trunk/packages/uc-echo/trunk/debian/watch
Log:
initial version of uc-echo
Property changes on: trunk/packages/uc-echo/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/uc-echo/trunk/debian/changelog
===
--- trunk/packages/uc-echo/trunk/debian/changelog
(rev 0)
+++ trunk/packages/uc-echo/trunk/debian/changelog 2013-04-07 14:33:19 UTC
(rev 13269)
@@ -0,0 +1,6 @@
+uc-echo (1.12-1) unstable; urgency=low
+
+ * initial version (Closes: #704902)
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 12 Mar 2013 18:00:07 +0100
+
Added: trunk/packages/uc-echo/trunk/debian/compat
===
--- trunk/packages/uc-echo/trunk/debian/compat (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/compat 2013-04-07 14:33:19 UTC (rev
13269)
@@ -0,0 +1 @@
+9
Added: trunk/packages/uc-echo/trunk/debian/control
===
--- trunk/packages/uc-echo/trunk/debian/control (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/control 2013-04-07 14:33:19 UTC (rev
13269)
@@ -0,0 +1,25 @@
+Source: uc-echo
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Thorsten Alteholz deb...@alteholz.de
+Build-Depends: debhelper (= 9),
+ python-all-dev (=2.6),
+ python-scipy,
+ python-numpy,
+ g++-multilib
+Standards-Version: 3.9.4
+Homepage: http://uc-echo.sourceforge.net/
+Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/uc-echo/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/uc-echo/trunk/
+
+Package: uc-echo
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: error correction algorithm designed for short-reads from NGS
+ ECHO is an error correction algorithm designed for short-reads
+ from next-generation sequencing platforms such as Illumina's
+ Genome Analyzer II. The algorithm uses a Bayesian framework to
+ improve the quality of the reads in a given data set by employing
+ maximum a posteriori estimation.
+
Added: trunk/packages/uc-echo/trunk/debian/copyright
===
--- trunk/packages/uc-echo/trunk/debian/copyright
(rev 0)
+++ trunk/packages/uc-echo/trunk/debian/copyright 2013-04-07 14:33:19 UTC
(rev 13269)
@@ -0,0 +1,32 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: uc-echo
+Source: http://uc-echo.sourceforge.net/
+
+Files: *
+Copyright: 2011, Yun S. Song
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+ .
+Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS
AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED
[med-svn] r13093 - in trunk/packages/vcftools/trunk/debian: . patches
Author: alteholz Date: 2013-02-24 15:33:43 + (Sun, 24 Feb 2013) New Revision: 13093 Added: trunk/packages/vcftools/trunk/debian/fill-fs.1 trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 trunk/packages/vcftools/trunk/debian/vcf-consensus.1 trunk/packages/vcftools/trunk/debian/vcf-contrast.1 trunk/packages/vcftools/trunk/debian/vcf-fix-ploidy.1 trunk/packages/vcftools/trunk/debian/vcf-indel-stats.1 trunk/packages/vcftools/trunk/debian/vcf-phased-join.1 trunk/packages/vcftools/trunk/debian/vcf-shuffle-cols.1 trunk/packages/vcftools/trunk/debian/vcf-tstv.1 trunk/packages/vcftools/trunk/debian/vcftools.lintian-overrides Modified: trunk/packages/vcftools/trunk/debian/changelog trunk/packages/vcftools/trunk/debian/manpages trunk/packages/vcftools/trunk/debian/patches/use-dpkg-buildflags.patch Log: preparation of new version Modified: trunk/packages/vcftools/trunk/debian/changelog === --- trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:31:06 UTC (rev 13092) +++ trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:33:43 UTC (rev 13093) @@ -1,10 +1,16 @@ -vcftools (0.1.10+dfsg-1) UNRELEASED; urgency=low +vcftools (0.1.10+dfsg-1) unstable; urgency=low + [ Thorsten Alteholz ] + * add man pages for new scripts + * debian/patches/use-dpkg-buildflags.patch: add LDFLAGS to link stage + * debian/vcftools.lintian-overrides: false positive + + [ Dominique Belhachemi ] * New upstream version - * Updated debian/use-dpkg-buildflags.patch - * Removed debian/perl.patch (applied upstream) + * Updated debian/patches/use-dpkg-buildflags.patch + * Removed debian/patches/perl.patch (applied upstream) - -- Dominique Belhachemi domi...@debian.org Tue, 19 Feb 2013 14:18:25 -0500 + -- Thorsten Alteholz deb...@alteholz.de Sun, 24 Feb 2013 16:00:00 +0100 vcftools (0.1.9+dfsg-2) unstable; urgency=low Added: trunk/packages/vcftools/trunk/debian/fill-fs.1 === --- trunk/packages/vcftools/trunk/debian/fill-fs.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/fill-fs.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,39 @@ +.\ DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH FILL-FS 1 February 2013 fill-fs User Commands +.SH NAME +fill-fs \- Annotate VCF with flanking sequence +.SH SYNOPSIS +.B fill-fs +[\fIOPTIONS\fR] \fIfile.vcf\fR +.SH DESCRIPTION +About: Annotate VCF with flanking sequence (INFO/FS tag) +.SH OPTIONS +.TP +\fB\-b\fR, \fB\-\-bed\-mask\fR file +Regions to mask (tabix indexed), multiple files can be given +.TP +\fB\-c\fR, \fB\-\-cluster\fR int +Do self\-masking of clustered variants within this range. +.TP +\fB\-l\fR, \fB\-\-length\fR int +Flanking sequence length [100] +.TP +\fB\-m\fR, \fB\-\-mask\-char\fR char|lc +The character to use or lc for lowercase. This option must preceed +\fB\-b\fR, \fB\-v\fR or \fB\-c\fR in order to take effect. With multiple files works +.IP +as a switch on the command line, see the example below [N] +.TP +\fB\-r\fR, \fB\-\-refseq\fR file +The reference sequence. +.TP +\fB\-v\fR, \fB\-\-vcf\-mask\fR file +Mask known variants in the flanking sequence, multiple files can be given (tabix indexed) +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SS Example: +.IP +# Mask variants from the VCF file with N's and use lowercase for the bed file regions +fill\-fs file.vcf \fB\-v\fR mask.vcf \fB\-m\fR lc \fB\-b\fR mask.bed +.IP Added: trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 === --- trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 (rev 0) +++ trunk/packages/vcftools/trunk/debian/fill-ref-md5.1 2013-02-24 15:33:43 UTC (rev 13093) @@ -0,0 +1,31 @@ +.\ DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH FILL-REF-MD5 1 February 2013 fill-ref-md5 User Commands +.SH NAME +fill-ref-md5 \- computes MD5 sum of the reference sequence +.SH SYNOPSIS +.B fill-ref-md5 +[\fIOPTIONS\fR] \fIin.vcf.gz out.vcf.gz\fR +.SH DESCRIPTION +About: The script computes MD5 sum of the reference sequence and inserts +.IP +\'reference' and 'contig' tags into header as recommended by VCFv4.1. +The VCF file must be compressed and tabix indexed, as it takes advantage +of the lightning fast tabix reheader functionality. +.SH OPTIONS +.TP +\fB\-d\fR, \fB\-\-dictionary\fR file +Where to read/write computed MD5s. Opened in append mode, existing records are not touched. +.TP +\fB\-i\fR, \fB\-\-info\fR AS:xx,SP:xx,TX:xx +Optional info on reference assembly (AS), species (SP), taxonomy (TX) +.TP +\fB\-r\fR, \fB\-\-refseq\fR file +The reference sequence in fasta format indexed by samtools faidx +.TP +\fB\-h\fR, \-?, \fB\-\-help\fR +This help message. +.SH EXAMPLES +.TP +fill\-ref\-md5 \-i AS:NCBIM37,SP:Mus\e Musculus \-r NCBIM37_um.fa
[med-svn] r13094 - trunk/packages/vcftools/trunk/debian
Author: alteholz Date: 2013-02-24 15:39:46 + (Sun, 24 Feb 2013) New Revision: 13094 Modified: trunk/packages/vcftools/trunk/debian/changelog trunk/packages/vcftools/trunk/debian/control Log: debian/control update Modified: trunk/packages/vcftools/trunk/debian/changelog === --- trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:33:43 UTC (rev 13093) +++ trunk/packages/vcftools/trunk/debian/changelog 2013-02-24 15:39:46 UTC (rev 13094) @@ -4,6 +4,8 @@ * add man pages for new scripts * debian/patches/use-dpkg-buildflags.patch: add LDFLAGS to link stage * debian/vcftools.lintian-overrides: false positive + * debian/control: standard bumped to 3.9.4 (no changes) + * debian/control: DM-Upload-Allowed removed [ Dominique Belhachemi ] * New upstream version Modified: trunk/packages/vcftools/trunk/debian/control === --- trunk/packages/vcftools/trunk/debian/control2013-02-24 15:33:43 UTC (rev 13093) +++ trunk/packages/vcftools/trunk/debian/control2013-02-24 15:39:46 UTC (rev 13094) @@ -2,10 +2,9 @@ Section: science Priority: extra Build-Depends: debhelper (= 9), zlib1g-dev -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://vcftools.sourceforge.net Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes Uploaders: Thorsten Alteholz deb...@alteholz.de, Andreas Tille ti...@debian.org Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vcftools/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13053 - trunk/packages/autodocksuite/trunk/debian
Author: alteholz Date: 2013-02-20 18:41:01 + (Wed, 20 Feb 2013) New Revision: 13053 Modified: trunk/packages/autodocksuite/trunk/debian/changelog trunk/packages/autodocksuite/trunk/debian/rules Log: remove lto flags again Modified: trunk/packages/autodocksuite/trunk/debian/changelog === --- trunk/packages/autodocksuite/trunk/debian/changelog 2013-02-20 09:28:55 UTC (rev 13052) +++ trunk/packages/autodocksuite/trunk/debian/changelog 2013-02-20 18:41:01 UTC (rev 13053) @@ -1,3 +1,9 @@ +autodocksuite (4.2.5.1-2) experimental; urgency=low + + * debian/rules: remove lto flags again, does not really work + + -- Thorsten Alteholz deb...@alteholz.de Wed, 20 Feb 2013 18:00:00 +0100 + autodocksuite (4.2.5.1-1) experimental; urgency=low * new upstream version Modified: trunk/packages/autodocksuite/trunk/debian/rules === --- trunk/packages/autodocksuite/trunk/debian/rules 2013-02-20 09:28:55 UTC (rev 13052) +++ trunk/packages/autodocksuite/trunk/debian/rules 2013-02-20 18:41:01 UTC (rev 13053) @@ -23,8 +23,9 @@ CFLAGS += -Wall -g # link time optimisation - as soon as gcc-4.5 hits the archive -CFLAGS += -flto -LDFLAGS += -flto +# 20.02.2013, ta, does not really work yet +#CFLAGS += -flto +#LDFLAGS += -flto ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13045 - in trunk/packages/autodocksuite/trunk/debian: . patches
Author: alteholz
Date: 2013-02-18 18:13:27 + (Mon, 18 Feb 2013)
New Revision: 13045
Modified:
trunk/packages/autodocksuite/trunk/debian/changelog
trunk/packages/autodocksuite/trunk/debian/control
trunk/packages/autodocksuite/trunk/debian/copyright
trunk/packages/autodocksuite/trunk/debian/patches/make.patch
trunk/packages/autodocksuite/trunk/debian/rules
Log:
ready for upload
Modified: trunk/packages/autodocksuite/trunk/debian/changelog
===
--- trunk/packages/autodocksuite/trunk/debian/changelog 2013-02-18 15:07:24 UTC
(rev 13044)
+++ trunk/packages/autodocksuite/trunk/debian/changelog 2013-02-18 18:13:27 UTC
(rev 13045)
@@ -1,8 +1,14 @@
-autodocksuite (4.2.5.1-1) UNRELEASED; urgency=low
+autodocksuite (4.2.5.1-1) experimental; urgency=low
* new upstream version
+ * add make.patch
+ * debian/copyright: point to GPL-2 instead of just GPL
+ * debian/control: add more description to autodock-test and autogrid-test
+ * debian/rules: add autodock/RELEASENOTES as upstream ChangeLog
+ * debian/rules: introduce hardening flags
+ * debian/rules: activate link time optimisation
- -- Thorsten Alteholz deb...@alteholz.de Sat, 16 Feb 2013 20:42:51 +0100
+ -- Thorsten Alteholz deb...@alteholz.de Mon, 18 Feb 2013 19:00:00 +0100
autodocksuite (4.2.3-3) UNRELEASED; urgency=low
Modified: trunk/packages/autodocksuite/trunk/debian/control
===
--- trunk/packages/autodocksuite/trunk/debian/control 2013-02-18 15:07:24 UTC
(rev 13044)
+++ trunk/packages/autodocksuite/trunk/debian/control 2013-02-18 18:13:27 UTC
(rev 13045)
@@ -48,6 +48,13 @@
Suggests: autodock
Depends: ${misc:Depends}
Description: test files for AutoDock
+ AutoDock is a prime representative of the programs addressing the
+ simulation of the docking of fairly small chemical ligands to rather big
+ protein receptors. Earlier versions had all flexibility in the ligands
+ while the protein was kept rather ridgid. This latest version 4 also
+ allows for a flexibility of selected sidechains of surface residues,
+ i.e., takes the rotamers into account.
+ .
This package contain the test files for the AutoDock program.
Package: autogrid-test
@@ -55,6 +62,10 @@
Suggests: autogrid
Depends: ${misc:Depends}
Description: test files for AutoGrid
+ The AutoDockSuite addresses the molecular analysis of the docking of
+ a smaller chemical compounds to their receptors of known three-dimensional
+ structure.
+ .
This package contain the test files for the AutoGrid program.
Package: autodock-getdata
Modified: trunk/packages/autodocksuite/trunk/debian/copyright
===
--- trunk/packages/autodocksuite/trunk/debian/copyright 2013-02-18 15:07:24 UTC
(rev 13044)
+++ trunk/packages/autodocksuite/trunk/debian/copyright 2013-02-18 18:13:27 UTC
(rev 13045)
@@ -56,7 +56,7 @@
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Public License can be found in `/usr/share/common-licenses/GPL-2'.
The Debian packaging is © 2007, Steffen Moeller moel...@debian.org and
is licensed under the GPL, see above.
Modified: trunk/packages/autodocksuite/trunk/debian/patches/make.patch
===
--- trunk/packages/autodocksuite/trunk/debian/patches/make.patch
2013-02-18 15:07:24 UTC (rev 13044)
+++ trunk/packages/autodocksuite/trunk/debian/patches/make.patch
2013-02-18 18:13:27 UTC (rev 13045)
@@ -1,3 +1,6 @@
+Description: adapt make process to Debian build environment
+Author: Thorsten Alteholz deb...@alteholz.de
+Last-Update: 2013-02-16
Index: src/autogrid/Makefile.am
===
--- src.orig/autogrid/Makefile.am 2013-02-17 18:47:22.0 +0100
Modified: trunk/packages/autodocksuite/trunk/debian/rules
===
--- trunk/packages/autodocksuite/trunk/debian/rules 2013-02-18 15:07:24 UTC
(rev 13044)
+++ trunk/packages/autodocksuite/trunk/debian/rules 2013-02-18 18:13:27 UTC
(rev 13045)
@@ -6,19 +6,25 @@
SHELL := /bin/bash
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
+
CXX=g++
CC=gcc
#CXX=/usr/lib/gcc-snapshot/bin/g++
#CC=/usr/lib/gcc-snapshot/bin/gcc
# see http://www.gentoo.org/proj/en/qa/asneeded.xml
-LDFLAGS=-Wl,--as-needed
+LDFLAGS+=-Wl,--as-needed
-CFLAGS = -Wall -g
+CFLAGS += -Wall -g
# link time optimisation - as soon as gcc-4.5 hits the archive
-#CFLAGS += -flto
-#LDFLAGS += -flto
+CFLAGS += -flto
+LDFLAGS += -flto
[med-svn] r12586 - trunk/packages/freemedforms-project/trunk/debian
Author: alteholz
Date: 2012-12-04 19:02:34 + (Tue, 04 Dec 2012)
New Revision: 12586
Modified:
trunk/packages/freemedforms-project/trunk/debian/changelog
trunk/packages/freemedforms-project/trunk/debian/control
Log:
fix typo
Modified: trunk/packages/freemedforms-project/trunk/debian/changelog
===
--- trunk/packages/freemedforms-project/trunk/debian/changelog 2012-12-04
13:09:35 UTC (rev 12585)
+++ trunk/packages/freemedforms-project/trunk/debian/changelog 2012-12-04
19:02:34 UTC (rev 12586)
@@ -1,3 +1,9 @@
+freemedforms-project (0.8.0-3) experimental; urgency=low
+
+ * debian/control: fix typo in dependency of freemedforms-libs
+
+ -- Thorsten Alteholz deb...@alteholz.de Tue, 04 Dec 2012 20:00:00 +0100
+
freemedforms-project (0.8.0-2) experimental; urgency=low
[ Eric Maeker ]
Modified: trunk/packages/freemedforms-project/trunk/debian/control
===
--- trunk/packages/freemedforms-project/trunk/debian/control2012-12-04
13:09:35 UTC (rev 12585)
+++ trunk/packages/freemedforms-project/trunk/debian/control2012-12-04
19:02:34 UTC (rev 12586)
@@ -151,7 +151,7 @@
Package: freemedforms-libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
- libqt4-sql (= 4:4.7.0),
+ libqt4-sql-mysql (= 4:4.7.0),
libqt4-sql-sqlite (= 4:4.7.0)
Description: common libs for the FreeMedForms project
The FreeMedForms project provides a set of medical applications to help
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[med-svn] r12580 - in trunk/packages/vcftools/trunk/debian: . patches
Author: alteholz
Date: 2012-12-02 18:08:04 + (Sun, 02 Dec 2012)
New Revision: 12580
Added:
trunk/packages/vcftools/trunk/debian/patches/perl.patch
Modified:
trunk/packages/vcftools/trunk/debian/changelog
trunk/packages/vcftools/trunk/debian/control
trunk/packages/vcftools/trunk/debian/get-orig-source
trunk/packages/vcftools/trunk/debian/patches/series
Log:
small improvements
Modified: trunk/packages/vcftools/trunk/debian/changelog
===
--- trunk/packages/vcftools/trunk/debian/changelog 2012-11-30 16:58:01 UTC
(rev 12579)
+++ trunk/packages/vcftools/trunk/debian/changelog 2012-12-02 18:08:04 UTC
(rev 12580)
@@ -1,3 +1,11 @@
+vcftools (0.1.9+dfsg-2) unstable; urgency=low
+
+ * debian/control: description changed (Closes: #689058)
+ * debian/patches/perl.patch for new syntax (Closes: #689059)
+ * fix get-orig-source to handle dfsg
+
+ -- Thorsten Alteholz deb...@alteholz.de Sun, 02 Dev 2012 19:00:00 +0100
+
vcftools (0.1.9+dfsg-1) UNRELEASED; urgency=low
* debian/copyright:
Modified: trunk/packages/vcftools/trunk/debian/control
===
--- trunk/packages/vcftools/trunk/debian/control2012-11-30 16:58:01 UTC
(rev 12579)
+++ trunk/packages/vcftools/trunk/debian/control2012-12-02 18:08:04 UTC
(rev 12580)
@@ -15,7 +15,7 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
Recommends: tabix
-Description: designed for working with VCF files
+Description: Collection of tools to work with VCF files
VCFtools is a program package designed for working with VCF files, such as
those generated by the 1000 Genomes Project. The aim of VCFtools is to
provide methods for working with VCF files: validating, merging, comparing
Modified: trunk/packages/vcftools/trunk/debian/get-orig-source
===
--- trunk/packages/vcftools/trunk/debian/get-orig-source2012-11-30
16:58:01 UTC (rev 12579)
+++ trunk/packages/vcftools/trunk/debian/get-orig-source2012-12-02
18:08:04 UTC (rev 12580)
@@ -20,6 +20,6 @@
find . -name *.pdf | xargs rm -f
cd ..
-GZIP=--best --no-name tar --owner=root --group=root --mode=a+rX -czf
$PKG_$DVERSION.orig.tar.gz ${PKG}_${DVERSION}
+GZIP=--best --no-name tar --owner=root --group=root --mode=a+rX -czf
$PKG_$DVERSION+dfsg.orig.tar.gz ${PKG}_${DVERSION}
rm -rf ${PKG}_${DVERSION}
Added: trunk/packages/vcftools/trunk/debian/patches/perl.patch
===
--- trunk/packages/vcftools/trunk/debian/patches/perl.patch
(rev 0)
+++ trunk/packages/vcftools/trunk/debian/patches/perl.patch 2012-12-02
18:08:04 UTC (rev 12580)
@@ -0,0 +1,15 @@
+Description: Don't use qw(...) as parentheses anymore (bad syntax now)
+Author: Thorsten Alteholz deb...@alteholz.de
+Index: vcftools_0.1.9/perl/Vcf.pm
+===
+--- vcftools_0.1.9.orig/perl/Vcf.pm2012-05-10 07:53:15.0 +0200
vcftools_0.1.9/perl/Vcf.pm 2012-12-02 18:55:40.0 +0100
+@@ -1619,7 +1619,7 @@
+ }
+ if ( defined $out )
+ {
+-for my $key qw(fmtA fmtG infoA infoG) { if ( !exists($$out{$key}) ) {
$$out{$key}=[] } }
++for my $key (qw(fmtA fmtG infoA infoG)) { if ( !exists($$out{$key}) )
{ $$out{$key}=[] } }
+ }
+ return $out;
+ }
Modified: trunk/packages/vcftools/trunk/debian/patches/series
===
--- trunk/packages/vcftools/trunk/debian/patches/series 2012-11-30 16:58:01 UTC
(rev 12579)
+++ trunk/packages/vcftools/trunk/debian/patches/series 2012-12-02 18:08:04 UTC
(rev 12580)
@@ -1,2 +1,3 @@
make.patch
use-dpkg-buildflags.patch
+perl.patch
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[med-svn] r12581 - trunk/packages/vcftools/trunk/debian
Author: alteholz Date: 2012-12-02 18:09:59 + (Sun, 02 Dec 2012) New Revision: 12581 Modified: trunk/packages/vcftools/trunk/debian/changelog Log: use correct name of month Modified: trunk/packages/vcftools/trunk/debian/changelog === --- trunk/packages/vcftools/trunk/debian/changelog 2012-12-02 18:08:04 UTC (rev 12580) +++ trunk/packages/vcftools/trunk/debian/changelog 2012-12-02 18:09:59 UTC (rev 12581) @@ -4,7 +4,7 @@ * debian/patches/perl.patch for new syntax (Closes: #689059) * fix get-orig-source to handle dfsg - -- Thorsten Alteholz deb...@alteholz.de Sun, 02 Dev 2012 19:00:00 +0100 + -- Thorsten Alteholz deb...@alteholz.de Sun, 02 Dec 2012 19:00:00 +0100 vcftools (0.1.9+dfsg-1) UNRELEASED; urgency=low ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12492 - trunk/packages/fasttree/trunk/debian
Author: alteholz Date: 2012-11-02 18:42:52 + (Fri, 02 Nov 2012) New Revision: 12492 Modified: trunk/packages/fasttree/trunk/debian/changelog Log: new upstream version Modified: trunk/packages/fasttree/trunk/debian/changelog === --- trunk/packages/fasttree/trunk/debian/changelog 2012-11-02 18:19:27 UTC (rev 12491) +++ trunk/packages/fasttree/trunk/debian/changelog 2012-11-02 18:42:52 UTC (rev 12492) @@ -1,3 +1,9 @@ +fasttree (2.1.5-1) unstable; urgency=low + + * New upstream version + + -- Thorsten Alteholz deb...@alteholz.de Fri, 02 Nov 2012 18:00:00 +0100 + fasttree (2.1.4-2) UNRELEASED; urgency=low * Fix name of upstream file and add eprint ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11873 - in trunk/packages/cluster3/trunk: . debian
Author: alteholz Date: 2012-07-23 17:41:47 + (Mon, 23 Jul 2012) New Revision: 11873 Removed: trunk/packages/cluster3/trunk/README.status Modified: trunk/packages/cluster3/trunk/debian/control Log: work on dependencies Deleted: trunk/packages/cluster3/trunk/README.status === --- trunk/packages/cluster3/trunk/README.status 2012-07-23 14:00:08 UTC (rev 11872) +++ trunk/packages/cluster3/trunk/README.status 2012-07-23 17:41:47 UTC (rev 11873) @@ -1,6 +0,0 @@ -Format: 1 -Status: draft -Comment: - Work on this project was started by Steffen M�ller but has stalled. - Feel free to take it over. Modified: trunk/packages/cluster3/trunk/debian/control === --- trunk/packages/cluster3/trunk/debian/control2012-07-23 14:00:08 UTC (rev 11872) +++ trunk/packages/cluster3/trunk/debian/control2012-07-23 17:41:47 UTC (rev 11873) @@ -5,9 +5,20 @@ Uploaders: Steffen Moeller moel...@debian.org, Charles Plessy ple...@debian.org, Thorsten Alteholz deb...@alteholz.de -Build-Depends: debhelper (= 9), libmotif-dev, autotools-dev, perl +Build-Depends: debhelper (= 9), + libmotif-dev, + autotools-dev, + perl, + libx11-dev, + libice-dev, + libxext-dev, + libsm-dev, + libxt-dev, + docbook-to-man Standards-Version: 3.9.3 Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cluster3/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cluster3/trunk/ Package: cluster3 Architecture: any ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11828 - in trunk/packages/cluster3/trunk/debian: . patches source
Author: alteholz Date: 2012-07-18 17:47:04 + (Wed, 18 Jul 2012) New Revision: 11828 Added: trunk/packages/cluster3/trunk/debian/cluster3.doc-base trunk/packages/cluster3/trunk/debian/patches/ trunk/packages/cluster3/trunk/debian/patches/compile-warnings.patch trunk/packages/cluster3/trunk/debian/patches/series trunk/packages/cluster3/trunk/debian/source/ trunk/packages/cluster3/trunk/debian/source/format trunk/packages/cluster3/trunk/debian/upstream Modified: trunk/packages/cluster3/trunk/debian/changelog trunk/packages/cluster3/trunk/debian/cluster3-doc.docs trunk/packages/cluster3/trunk/debian/cluster3.docs trunk/packages/cluster3/trunk/debian/compat trunk/packages/cluster3/trunk/debian/control trunk/packages/cluster3/trunk/debian/copyright trunk/packages/cluster3/trunk/debian/menu trunk/packages/cluster3/trunk/debian/rules Log: cluster3 almost finished now Modified: trunk/packages/cluster3/trunk/debian/changelog === --- trunk/packages/cluster3/trunk/debian/changelog 2012-07-18 09:31:37 UTC (rev 11827) +++ trunk/packages/cluster3/trunk/debian/changelog 2012-07-18 17:47:04 UTC (rev 11828) @@ -1,7 +1,5 @@ -cluster3 (1.50-1) UNRELEASED; urgency=low +cluster3 (1.50-1) unstable; urgency=low - * XXX TODO: before uploading the ITP needs to be reopened - [ Thorsten Alteholz ] * New upstream release (1.50). * debian/rules: target get-orig-source added @@ -14,17 +12,17 @@ [ Charles Plessy ] * Initial release. * Manpage built before source package generation, removed docbook-to-man -build dependancy. +build dependency. - -- DMPT debian-med-packag...@lists.alioth.debian.org Fri, 01 Aug 2008 13:29:25 +0900 + -- Thorsten Alteholz deb...@alteholz.de Wed, 18 Jul 2012 18:00:00 +0200 -cluster3 (1.25-0.2) unstable; urgency=low +cluster3 (1.25-0.2) UNRELEASED; urgency=low * Provides both the motif gui and command line interface. -- Steffen Moeller moel...@pzr.uni-rostock.de Tue, 7 Apr 2004 18:31:37 +0200 -cluster3 (1.25-0.1) unstable; urgency=low +cluster3 (1.25-0.1) UNRELEASED; urgency=low * Initial Release. Modified: trunk/packages/cluster3/trunk/debian/cluster3-doc.docs === --- trunk/packages/cluster3/trunk/debian/cluster3-doc.docs 2012-07-18 09:31:37 UTC (rev 11827) +++ trunk/packages/cluster3/trunk/debian/cluster3-doc.docs 2012-07-18 17:47:04 UTC (rev 11828) @@ -3,3 +3,5 @@ docs/cluster3.pdf docs/cluster3.texinfo docs/structure.eps +html/*.html +html/images/* Added: trunk/packages/cluster3/trunk/debian/cluster3.doc-base === --- trunk/packages/cluster3/trunk/debian/cluster3.doc-base (rev 0) +++ trunk/packages/cluster3/trunk/debian/cluster3.doc-base 2012-07-18 17:47:04 UTC (rev 11828) @@ -0,0 +1,24 @@ +Document: cluster3 +Title: Cluster 3.0 for Windows, Mac OS X, Linux, Unix +Author: Michael Eisen; updated by Michiel de Hoon +Abstract: This is the manual for Cluster 3.0. + Cluster was originally written by Michael Eisen while at Stanford + University. We have modified the clustering algorithm in Cluster, + and extended the algorithm for Self-Organizing Maps to include + two-dimensional rectangular grids. The Euclidean distance and the + city-block distance were added as new distance measures between gene + expression data. The proprietary Numerical Recipes routines, which + were used in the original version of Cluster/TreeView, have been + replaced by open source software. + . + Cluster 3.0 is available for Windows, Mac OS X, Linux, and Unix. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/cluster3/cluster.pdf.gz + /usr/share/doc/cluster3/cluster3.pdf.gz + +Format: html +Index: /usr/share/doc/cluster3/html/index.html +Files: /usr/share/doc/cluster3/html/*.html + Modified: trunk/packages/cluster3/trunk/debian/cluster3.docs === --- trunk/packages/cluster3/trunk/debian/cluster3.docs 2012-07-18 09:31:37 UTC (rev 11827) +++ trunk/packages/cluster3/trunk/debian/cluster3.docs 2012-07-18 17:47:04 UTC (rev 11828) @@ -1,2 +1,3 @@ NEWS README +html/ Modified: trunk/packages/cluster3/trunk/debian/compat === --- trunk/packages/cluster3/trunk/debian/compat 2012-07-18 09:31:37 UTC (rev 11827) +++ trunk/packages/cluster3/trunk/debian/compat 2012-07-18 17:47:04 UTC (rev 11828) @@ -1 +1 @@ -4 +9 Modified: trunk/packages/cluster3/trunk/debian/control === --- trunk/packages/cluster3/trunk/debian/control2012-07-18 09:31:37 UTC (rev 11827) +++ trunk/packages/cluster3/trunk/debian/control2012-07-18 17:47:04 UTC (rev 11828) @@ -2,9 +2,11
[med-svn] r11375 - in trunk/packages/meme/trunk: . debian
Author: alteholz
Date: 2012-06-18 18:02:25 + (Mon, 18 Jun 2012)
New Revision: 11375
Removed:
trunk/packages/meme/trunk/README.status
Modified:
trunk/packages/meme/trunk/debian/control
trunk/packages/meme/trunk/debian/meme-examples.install
trunk/packages/meme/trunk/debian/rules
Log:
more progress, less lintian complaints
Deleted: trunk/packages/meme/trunk/README.status
===
--- trunk/packages/meme/trunk/README.status 2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/README.status 2012-06-18 18:02:25 UTC (rev
11375)
@@ -1,7 +0,0 @@
-Format: 1
-Status: draft
-Comment:
- Work on this project was started by Steffen Möller but has stalled.
- It is continued by H. Soon Gweon soo...@gmail.com and
- Andreas Tille ti...@debian.org
Modified: trunk/packages/meme/trunk/debian/control
===
--- trunk/packages/meme/trunk/debian/control2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/debian/control2012-06-18 18:02:25 UTC (rev
11375)
@@ -6,7 +6,10 @@
Uploaders: Andreas Tille ti...@debian.org,
H. Soon Gweon soo...@gmail.com,
Thorsten Alteholz deb...@alteholz.de
-Build-Depends: debhelper (= 9), dh-autoreconf, libxslt1-dev
+Build-Depends: debhelper (= 9),
+ dh-autoreconf,
+ libxslt1-dev,
+ python-all (= 2.6.6-3~)
Standards-Version: 3.9.3
Homepage: http://meme.nbcr.net/meme/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/meme/trunk/
@@ -35,11 +38,13 @@
Recommends: meme
Depends: ${misc:Depends}
Description: Example files for the MEME motif searcher
- This package includes the example files that come with MEME
+ This package includes the example files that come with MEME. They can be used
+ to either check the functionality of the software or play around with the
+ possibilities.
Package: glam2
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
Description: gapped protein motifs from unaligned sequences
GLAM2 is a software package for finding motifs in sequences, typically
amino-acid or nucleotide sequences. A motif is a re-occurring sequence
Modified: trunk/packages/meme/trunk/debian/meme-examples.install
===
--- trunk/packages/meme/trunk/debian/meme-examples.install 2012-06-18
09:09:29 UTC (rev 11374)
+++ trunk/packages/meme/trunk/debian/meme-examples.install 2012-06-18
18:02:25 UTC (rev 11375)
@@ -1 +1 @@
-/examples /usr/share/doc/meme/examples
+/examples /usr/share/doc/meme
Modified: trunk/packages/meme/trunk/debian/rules
===
--- trunk/packages/meme/trunk/debian/rules 2012-06-18 09:09:29 UTC (rev
11374)
+++ trunk/packages/meme/trunk/debian/rules 2012-06-18 18:02:25 UTC (rev
11375)
@@ -1,13 +1,14 @@
#!/usr/bin/make -f
# debian/rules file for meme
# Andreas Tille ti...@debian.org
+# Thorsten Alteholz deb...@alteholz.de
# GPL
DBPATH=/var/lib/meme
LOGPATH=/var/log/meme
%:
- dh $@ --with autoreconf
+ dh $@ --with autoreconf,python2
override_dh_auto_configure:
./configure --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --sysconfdir=/etc/meme \
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[med-svn] r11357 - in trunk/packages/fasttree/trunk/debian: . patches
Author: alteholz Date: 2012-06-15 18:05:04 + (Fri, 15 Jun 2012) New Revision: 11357 Added: trunk/packages/fasttree/trunk/debian/fasttree.1 trunk/packages/fasttree/trunk/debian/fasttree.upstream-metadata.yaml trunk/packages/fasttree/trunk/debian/fasttreeMP.1 trunk/packages/fasttree/trunk/debian/get-orig-source trunk/packages/fasttree/trunk/debian/manpages trunk/packages/fasttree/trunk/debian/watch Removed: trunk/packages/fasttree/trunk/debian/README.Debian Modified: trunk/packages/fasttree/trunk/debian/changelog trunk/packages/fasttree/trunk/debian/compat trunk/packages/fasttree/trunk/debian/control trunk/packages/fasttree/trunk/debian/copyright trunk/packages/fasttree/trunk/debian/fasttree.install trunk/packages/fasttree/trunk/debian/patches/Makefile.patch trunk/packages/fasttree/trunk/debian/rules Log: fasttree finalized Deleted: trunk/packages/fasttree/trunk/debian/README.Debian === --- trunk/packages/fasttree/trunk/debian/README.Debian 2012-06-15 14:31:56 UTC (rev 11356) +++ trunk/packages/fasttree/trunk/debian/README.Debian 2012-06-15 18:05:04 UTC (rev 11357) @@ -1,9 +0,0 @@ -fasttree for Debian - -Please help with - - * man pages - * get-orig-source - upstream is only a file - - -- Steffen Moeller moel...@debian.org Wed, 02 Mar 2011 18:52:56 +0100 Modified: trunk/packages/fasttree/trunk/debian/changelog === --- trunk/packages/fasttree/trunk/debian/changelog 2012-06-15 14:31:56 UTC (rev 11356) +++ trunk/packages/fasttree/trunk/debian/changelog 2012-06-15 18:05:04 UTC (rev 11357) @@ -1,5 +1,5 @@ -fasttree (2.1.0.c-1) UNRELEASED; urgency=low +fasttree (2.1.4-1) unstable; urgency=low - * Initial release (Closes: #) is the bug number of your ITP + * Initial release (Closes: #677648) - -- Steffen Moeller moel...@debian.org Wed, 02 Mar 2011 18:52:56 +0100 + -- Thorsten Alteholz deb...@alteholz.de Fri, 15 Jun 2012 19:52:56 +0200 Modified: trunk/packages/fasttree/trunk/debian/compat === --- trunk/packages/fasttree/trunk/debian/compat 2012-06-15 14:31:56 UTC (rev 11356) +++ trunk/packages/fasttree/trunk/debian/compat 2012-06-15 18:05:04 UTC (rev 11357) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/fasttree/trunk/debian/control === --- trunk/packages/fasttree/trunk/debian/control2012-06-15 14:31:56 UTC (rev 11356) +++ trunk/packages/fasttree/trunk/debian/control2012-06-15 18:05:04 UTC (rev 11357) @@ -3,9 +3,10 @@ Priority: extra Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org DM-Upload-Allowed: yes -Uploaders: Steffen Moeller moel...@debian.org -Build-Depends: debhelper (= 7.0.50~) -Standards-Version: 3.9.1 +Uploaders: Steffen Moeller moel...@debian.org, + Thorsten Alteholz deb...@alteholz.de +Build-Depends: debhelper (= 9) +Standards-Version: 3.9.3 Homepage: http://www.microbesonline.org/fasttree/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/ @@ -28,5 +29,8 @@ for the varying rates of evolution across sites, FastTree uses a single rate for each site (the CAT approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support - values with the Shimodaira-Hasegawa test (these are the same as PhyML - 3's SH-like local supports). + values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's + SH-like local supports). + . + This package contains a single threaded version (fasttree) and a + parallel version which uses OpenMP (fasttreMP). Modified: trunk/packages/fasttree/trunk/debian/copyright === --- trunk/packages/fasttree/trunk/debian/copyright 2012-06-15 14:31:56 UTC (rev 11356) +++ trunk/packages/fasttree/trunk/debian/copyright 2012-06-15 18:05:04 UTC (rev 11357) @@ -8,6 +8,7 @@ Files: debian/* Copyright: 2011 Steffen Moeller moel...@debian.org + 2012 Thorsten Alteholz deb...@alteholz.de License: GPL-2.0+ License: GPL-2.0+ Added: trunk/packages/fasttree/trunk/debian/fasttree.1 === --- trunk/packages/fasttree/trunk/debian/fasttree.1 (rev 0) +++ trunk/packages/fasttree/trunk/debian/fasttree.1 2012-06-15 18:05:04 UTC (rev 11357) @@ -0,0 +1,339 @@ +.TH fasttree 1 June 2012 Lawrence Berkeley National Lab User Commands +.SH NAME +fasttree \- create phylogenetic trees from alignments of nucleotide or protein sequences +.SH DESCRIPTION +fasttree infers approximately-maximum-likelihood phylogenetic trees from +alignments of nucleotide or protein
[med-svn] r11309 - trunk/packages/plastimatch/trunk/debian
Author: alteholz
Date: 2012-06-12 20:30:19 + (Tue, 12 Jun 2012)
New Revision: 11309
Modified:
trunk/packages/plastimatch/trunk/debian/control
trunk/packages/plastimatch/trunk/debian/copyright
Log:
debhelper dependency needed in control as well, some additions to copyright to
calm lintian
Modified: trunk/packages/plastimatch/trunk/debian/control
===
--- trunk/packages/plastimatch/trunk/debian/control 2012-06-12 02:15:06 UTC
(rev 11308)
+++ trunk/packages/plastimatch/trunk/debian/control 2012-06-12 20:30:19 UTC
(rev 11309)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Gregory C. Sharp gregsharp@yahoo.com, Dominique Belhachemi
domi...@debian.org
-Build-Depends: debhelper (= 8), cmake,
+Build-Depends: debhelper (= 9), cmake,
gfortran,
libdcmtk2-dev (= 3.6.0-10),
libfftw3-dev,
@@ -20,7 +20,6 @@
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/plastimatch/trunk
Package: plastimatch
-Section: science
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: medical image reconstruction and registration
Modified: trunk/packages/plastimatch/trunk/debian/copyright
===
--- trunk/packages/plastimatch/trunk/debian/copyright 2012-06-12 02:15:06 UTC
(rev 11308)
+++ trunk/packages/plastimatch/trunk/debian/copyright 2012-06-12 20:30:19 UTC
(rev 11309)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: plastimatch
Upstream-Contact: Gregory C. Sharp gregsharp@yahoo.com
Source: http://plastimatch.org
@@ -121,35 +121,205 @@
Files: debian/*
Copyright: 2011 Gregory C. Sharp gregsharp@yahoo.com
License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+(3) Neither the name of Georgetown University nor the
+names of its contributors may be used to endorse or promote products
+derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS
AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Files: libs/bstrlib-05122010/*
Copyright: 2002-2008 Paul Hsieh
License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+(3) Neither the name of Georgetown University nor the
+names of its contributors may be used to endorse or promote products
+derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS
AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
[med-svn] r11164 - in trunk/packages/mgltools: bhtree/trunk/debian geomutils/trunk/debian gle/trunk/debian opengltk/trunk/debian pyglf/trunk/debian sff/trunk/debian utpackages/trunk/debian vision/trun
Author: alteholz Date: 2012-06-01 21:01:54 + (Fri, 01 Jun 2012) New Revision: 11164 Modified: trunk/packages/mgltools/bhtree/trunk/debian/changelog trunk/packages/mgltools/bhtree/trunk/debian/control trunk/packages/mgltools/bhtree/trunk/debian/rules trunk/packages/mgltools/geomutils/trunk/debian/changelog trunk/packages/mgltools/geomutils/trunk/debian/control trunk/packages/mgltools/geomutils/trunk/debian/rules trunk/packages/mgltools/gle/trunk/debian/changelog trunk/packages/mgltools/gle/trunk/debian/control trunk/packages/mgltools/gle/trunk/debian/rules trunk/packages/mgltools/opengltk/trunk/debian/changelog trunk/packages/mgltools/opengltk/trunk/debian/control trunk/packages/mgltools/opengltk/trunk/debian/rules trunk/packages/mgltools/pyglf/trunk/debian/changelog trunk/packages/mgltools/pyglf/trunk/debian/control trunk/packages/mgltools/pyglf/trunk/debian/rules trunk/packages/mgltools/sff/trunk/debian/changelog trunk/packages/mgltools/sff/trunk/debian/control trunk/packages/mgltools/sff/trunk/debian/rules trunk/packages/mgltools/utpackages/trunk/debian/changelog trunk/packages/mgltools/utpackages/trunk/debian/control trunk/packages/mgltools/utpackages/trunk/debian/copyright trunk/packages/mgltools/utpackages/trunk/debian/rules trunk/packages/mgltools/vision/trunk/debian/changelog trunk/packages/mgltools/vision/trunk/debian/control trunk/packages/mgltools/vision/trunk/debian/rules trunk/packages/mgltools/visionlibraries/trunk/debian/changelog trunk/packages/mgltools/visionlibraries/trunk/debian/control trunk/packages/mgltools/visionlibraries/trunk/debian/rules Log: taking care of lintian errors and missing dependencies Modified: trunk/packages/mgltools/bhtree/trunk/debian/changelog === --- trunk/packages/mgltools/bhtree/trunk/debian/changelog 2012-06-01 16:21:16 UTC (rev 11163) +++ trunk/packages/mgltools/bhtree/trunk/debian/changelog 2012-06-01 21:01:54 UTC (rev 11164) @@ -1,3 +1,11 @@ +mgltools-bhtree (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low + + * New upstream version. + * debian/rules: add call to dh_numpy + * debian/control: bump standard to 3.9.3 + + -- Thorsten Alteholz deb...@alteholz.de Fri, 01 Jun 2012 18:00:00 +0200 + mgltools-bhtree (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. Modified: trunk/packages/mgltools/bhtree/trunk/debian/control === --- trunk/packages/mgltools/bhtree/trunk/debian/control 2012-06-01 16:21:16 UTC (rev 11163) +++ trunk/packages/mgltools/bhtree/trunk/debian/control 2012-06-01 21:01:54 UTC (rev 11164) @@ -9,7 +9,7 @@ Andreas Tille ti...@debian.org, Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 8), python-all-dev (= 2.6), python-numpy, swig (= 1.3.20) -Standards-Version: 3.9.2 +Standards-Version: 3.9.3 XS-Python-Version: = 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/bhtree/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/bhtree/trunk/ Modified: trunk/packages/mgltools/bhtree/trunk/debian/rules === --- trunk/packages/mgltools/bhtree/trunk/debian/rules 2012-06-01 16:21:16 UTC (rev 11163) +++ trunk/packages/mgltools/bhtree/trunk/debian/rules 2012-06-01 21:01:54 UTC (rev 11164) @@ -26,6 +26,10 @@ python$$i setup.py install --install-platlib=`pwd`/debian/tmpbuild; \ done +override_dh_install: + dh_install + dh_numpy + get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) Modified: trunk/packages/mgltools/geomutils/trunk/debian/changelog === --- trunk/packages/mgltools/geomutils/trunk/debian/changelog2012-06-01 16:21:16 UTC (rev 11163) +++ trunk/packages/mgltools/geomutils/trunk/debian/changelog2012-06-01 21:01:54 UTC (rev 11164) @@ -1,3 +1,11 @@ +mgltools-geomutils (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low + + * New upstream version. + * debian/rules: add call to dh_numpy + * debian/control: bump standard to 3.9.3 + + -- Thorsten Alteholz deb...@alteholz.de Fri, 01 Jun 2012 18:00:00 +0200 + mgltools-geomutils (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. Modified: trunk/packages/mgltools/geomutils/trunk/debian/control === --- trunk/packages/mgltools/geomutils/trunk/debian/control 2012-06-01 16:21:16 UTC (rev 11163) +++ trunk/packages/mgltools/geomutils/trunk/debian/control 2012-06-01 21:01:54 UTC (rev 11164) @@ -9,7 +9,7 @@ Andreas Tille ti...@debian.org, Thorsten Alteholz deb...@alteholz.de Build-Depends: debhelper (= 8), python-all-dev (= 2.6), swig, python-numpy
[med-svn] r10349 - trunk/packages/libsbml/trunk/debian
Author: alteholz Date: 2012-04-05 20:22:12 + (Thu, 05 Apr 2012) New Revision: 10349 Modified: trunk/packages/libsbml/trunk/debian/changelog trunk/packages/libsbml/trunk/debian/control trunk/packages/libsbml/trunk/debian/control.in Log: use dependency on swig only Modified: trunk/packages/libsbml/trunk/debian/changelog === --- trunk/packages/libsbml/trunk/debian/changelog 2012-04-05 19:47:01 UTC (rev 10348) +++ trunk/packages/libsbml/trunk/debian/changelog 2012-04-05 20:22:12 UTC (rev 10349) @@ -1,3 +1,11 @@ +libsbml (5.4.1-3) unstable; urgency=low + + * debian/control: removed dependency on swig2.0 (Closes: #667652) +thanks to Peter Green for the hint. + * debian/control: added myself to uploaders + + -- Thorsten Alteholz deb...@alteholz.de Thu, 05 Apr 2012 18:44:30 +0200 + libsbml (5.4.1-2) unstable; urgency=low * added a patch to correct misspelled words in th source Modified: trunk/packages/libsbml/trunk/debian/control === --- trunk/packages/libsbml/trunk/debian/control 2012-04-05 19:47:01 UTC (rev 10348) +++ trunk/packages/libsbml/trunk/debian/control 2012-04-05 20:22:12 UTC (rev 10349) @@ -4,12 +4,13 @@ Uploaders: Ivo Maintz i...@maintz.de, Changyan Xie panch...@gmail.com, Moriyoshi Koizumi m...@sfc.keio.ac.jp, - Andreas Tille ti...@debian.org + Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de DM-Upload-Allowed: yes Build-Depends: autoconf, automake, debhelper (= 8), - swig2.0 | swig (= 2), + swig (= 2), ruby1.8, libxml2-dev, python-dev, Modified: trunk/packages/libsbml/trunk/debian/control.in === --- trunk/packages/libsbml/trunk/debian/control.in 2012-04-05 19:47:01 UTC (rev 10348) +++ trunk/packages/libsbml/trunk/debian/control.in 2012-04-05 20:22:12 UTC (rev 10349) @@ -4,12 +4,13 @@ Uploaders: Ivo Maintz i...@maintz.de, Changyan Xie panch...@gmail.com, Moriyoshi Koizumi m...@sfc.keio.ac.jp, - Andreas Tille ti...@debian.org + Andreas Tille ti...@debian.org, + Thorsten Alteholz deb...@alteholz.de DM-Upload-Allowed: yes Build-Depends: autoconf, automake, debhelper (= 8), - swig2.0 | swig (= 2), + swig (= 2), ruby1.8, libxml2-dev, python-dev, ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10326 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz Date: 2012-04-04 19:53:40 + (Wed, 04 Apr 2012) New Revision: 10326 Modified: trunk/packages/R/r-cran-deal/trunk/debian/copyright Log: format can have real version now Modified: trunk/packages/R/r-cran-deal/trunk/debian/copyright === --- trunk/packages/R/r-cran-deal/trunk/debian/copyright 2012-04-04 15:59:56 UTC (rev 10325) +++ trunk/packages/R/r-cran-deal/trunk/debian/copyright 2012-04-04 19:53:40 UTC (rev 10326) @@ -1,4 +1,4 @@ -Format: http://dep.debian.net/deps/dep5 +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: deal Source: http://cran.r-project.org/src/contrib/deal_1.2-34.tar.gz ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10327 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz Date: 2012-04-04 19:55:57 + (Wed, 04 Apr 2012) New Revision: 10327 Modified: trunk/packages/R/r-cran-deal/trunk/debian/changelog Log: upload to unstable Modified: trunk/packages/R/r-cran-deal/trunk/debian/changelog === --- trunk/packages/R/r-cran-deal/trunk/debian/changelog 2012-04-04 19:53:40 UTC (rev 10326) +++ trunk/packages/R/r-cran-deal/trunk/debian/changelog 2012-04-04 19:55:57 UTC (rev 10327) @@ -1,4 +1,4 @@ -r-cran-deal (1.2.34-1) UNRELEASED; urgency=low +r-cran-deal (1.2.34-1) unstable; urgency=low * Initial release (closes: #659043) ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10328 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz Date: 2012-04-04 19:58:01 + (Wed, 04 Apr 2012) New Revision: 10328 Modified: trunk/packages/R/r-cran-deal/trunk/debian/changelog Log: timestamp is important here Modified: trunk/packages/R/r-cran-deal/trunk/debian/changelog === --- trunk/packages/R/r-cran-deal/trunk/debian/changelog 2012-04-04 19:55:57 UTC (rev 10327) +++ trunk/packages/R/r-cran-deal/trunk/debian/changelog 2012-04-04 19:58:01 UTC (rev 10328) @@ -2,4 +2,4 @@ * Initial release (closes: #659043) - -- ivo Maintz i...@maintz.de Wed, 01 Feb 2012 09:59:12 +0100 + -- ivo Maintz i...@maintz.de Wed, 04 Apr 2012 21:45:02 +0200 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10288 - trunk/packages/libsbml/trunk/debian
Author: alteholz Date: 2012-04-03 17:16:20 + (Tue, 03 Apr 2012) New Revision: 10288 Modified: trunk/packages/libsbml/trunk/debian/changelog Log: prepare release Modified: trunk/packages/libsbml/trunk/debian/changelog === --- trunk/packages/libsbml/trunk/debian/changelog 2012-04-03 16:01:36 UTC (rev 10287) +++ trunk/packages/libsbml/trunk/debian/changelog 2012-04-03 17:16:20 UTC (rev 10288) @@ -1,4 +1,4 @@ -libsbml (5.4.1-2) UNRELEASED; urgency=low +libsbml (5.4.1-2) unstable; urgency=low * added a patch to correct misspelled words in th source * debian/rules: ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10250 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz Date: 2012-04-02 17:52:21 + (Mon, 02 Apr 2012) New Revision: 10250 Modified: trunk/packages/R/r-cran-deal/trunk/debian/control Log: debian/control: tag fixed Modified: trunk/packages/R/r-cran-deal/trunk/debian/control === --- trunk/packages/R/r-cran-deal/trunk/debian/control 2012-04-02 14:48:29 UTC (rev 10249) +++ trunk/packages/R/r-cran-deal/trunk/debian/control 2012-04-02 17:52:21 UTC (rev 10250) @@ -3,7 +3,7 @@ Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Uploaders: ivo Maintz i...@maintz.de -DM-Upload-Allow: yes +DM-Upload-Allowed: yes Build-Depends: debhelper (= 8), r-base, r-base-dev, cdbs Standards-Version: 3.9.2 Homepage: http://cran.r-project.org/web/packages/deal/index.html ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10251 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz Date: 2012-04-02 17:58:36 + (Mon, 02 Apr 2012) New Revision: 10251 Modified: trunk/packages/R/r-cran-deal/trunk/debian/control Log: debian/control: standards version 3.9.3 Modified: trunk/packages/R/r-cran-deal/trunk/debian/control === --- trunk/packages/R/r-cran-deal/trunk/debian/control 2012-04-02 17:52:21 UTC (rev 10250) +++ trunk/packages/R/r-cran-deal/trunk/debian/control 2012-04-02 17:58:36 UTC (rev 10251) @@ -5,7 +5,7 @@ Uploaders: ivo Maintz i...@maintz.de DM-Upload-Allowed: yes Build-Depends: debhelper (= 8), r-base, r-base-dev, cdbs -Standards-Version: 3.9.2 +Standards-Version: 3.9.3 Homepage: http://cran.r-project.org/web/packages/deal/index.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-deal/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-deal/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10252 - trunk/packages/R/r-cran-deal/trunk/debian
Author: alteholz
Date: 2012-04-02 18:00:24 + (Mon, 02 Apr 2012)
New Revision: 10252
Modified:
trunk/packages/R/r-cran-deal/trunk/debian/get-orig-source
trunk/packages/R/r-cran-deal/trunk/debian/rules
Log:
debian/rules: add target get-orig-source and move tar to ../tarballs
Modified: trunk/packages/R/r-cran-deal/trunk/debian/get-orig-source
===
--- trunk/packages/R/r-cran-deal/trunk/debian/get-orig-source 2012-04-02
17:58:36 UTC (rev 10251)
+++ trunk/packages/R/r-cran-deal/trunk/debian/get-orig-source 2012-04-02
18:00:24 UTC (rev 10252)
@@ -13,5 +13,6 @@
chmod -x ${TARDIR}/CHANGELOG ${TARDIR}/DESCRIPTION ${TARDIR}/INDEX
${TARDIR}/NAMESPACE
GZIP=--best --no-name tar --owner=root --group=root --mode=a+rX -czf
$NAME_$VERSION.orig.tar.gz ${TARDIR}
rm -rf ${TARDIR} ${UPSTREAM_TARBALL}
-mv ${NAME}_${VERSION}.orig.tar.gz ../
+mkdir -p ../tarballs
+mv ${NAME}_${VERSION}.orig.tar.gz ../tarballs
Modified: trunk/packages/R/r-cran-deal/trunk/debian/rules
===
--- trunk/packages/R/r-cran-deal/trunk/debian/rules 2012-04-02 17:58:36 UTC
(rev 10251)
+++ trunk/packages/R/r-cran-deal/trunk/debian/rules 2012-04-02 18:00:24 UTC
(rev 10252)
@@ -3,3 +3,6 @@
include /usr/share/R/debian/r-cran.mk
#%:
# dh $@
+
+get-orig-source:
+ ./debian/get-orig-source
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[med-svn] r10207 - trunk/packages/rostlab/librostlab/trunk/debian
Author: alteholz Date: 2012-03-30 17:09:20 + (Fri, 30 Mar 2012) New Revision: 10207 Modified: trunk/packages/rostlab/librostlab/trunk/debian/watch Log: make it accessible from more sites Modified: trunk/packages/rostlab/librostlab/trunk/debian/watch === --- trunk/packages/rostlab/librostlab/trunk/debian/watch2012-03-30 16:43:37 UTC (rev 10206) +++ trunk/packages/rostlab/librostlab/trunk/debian/watch2012-03-30 17:09:20 UTC (rev 10207) @@ -1,4 +1,5 @@ # Compulsory line, this is a version 3 file version=3 +opts=passive \ ftp://rostlab.org/free/librostlab-([0-9.]+)\.tar\.gz debian uupdate ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10208 - trunk/packages/rostlab/librostlab-blast/trunk/debian
Author: alteholz Date: 2012-03-30 17:10:08 + (Fri, 30 Mar 2012) New Revision: 10208 Modified: trunk/packages/rostlab/librostlab-blast/trunk/debian/watch Log: make it accessible from more sites Modified: trunk/packages/rostlab/librostlab-blast/trunk/debian/watch === --- trunk/packages/rostlab/librostlab-blast/trunk/debian/watch 2012-03-30 17:09:20 UTC (rev 10207) +++ trunk/packages/rostlab/librostlab-blast/trunk/debian/watch 2012-03-30 17:10:08 UTC (rev 10208) @@ -1,4 +1,5 @@ # Compulsory line, this is a version 3 file version=3 +opts=passive \ ftp://rostlab.org/free/librostlab-blast-([0-9.]+)\.tar\.gz debian uupdate ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10209 - trunk/packages/rostlab/librostlab-blast/trunk/debian
Author: alteholz Date: 2012-03-30 17:10:49 + (Fri, 30 Mar 2012) New Revision: 10209 Modified: trunk/packages/rostlab/librostlab-blast/trunk/debian/copyright Log: we have versioned copyright now Modified: trunk/packages/rostlab/librostlab-blast/trunk/debian/copyright === --- trunk/packages/rostlab/librostlab-blast/trunk/debian/copyright 2012-03-30 17:10:08 UTC (rev 10208) +++ trunk/packages/rostlab/librostlab-blast/trunk/debian/copyright 2012-03-30 17:10:49 UTC (rev 10209) @@ -1,4 +1,4 @@ -Format: http://dep.debian.net/deps/dep5 +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: librostlab-blast Upstream-Contact: Laszlo Kajan lka...@rostlab.org Source: http://rostlab.org/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10210 - trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian
Author: alteholz Date: 2012-03-30 17:11:52 + (Fri, 30 Mar 2012) New Revision: 10210 Modified: trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/watch Log: make it accessible from more sites Modified: trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/watch === --- trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/watch 2012-03-30 17:10:49 UTC (rev 10209) +++ trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/watch 2012-03-30 17:11:52 UTC (rev 10210) @@ -1,4 +1,5 @@ # Compulsory line, this is a version 3 file version=3 +opts=passive \ ftp://rostlab.org/free/RG-Blast-Parser-([0-9.]+)\.tar\.gz debian uupdate ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r10211 - trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian
Author: alteholz Date: 2012-03-30 17:12:05 + (Fri, 30 Mar 2012) New Revision: 10211 Modified: trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/copyright Log: we have versioned copyright now Modified: trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/copyright === --- trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/copyright 2012-03-30 17:11:52 UTC (rev 10210) +++ trunk/packages/rostlab/librg-blast-parser-perl/trunk/debian/copyright 2012-03-30 17:12:05 UTC (rev 10211) @@ -1,4 +1,4 @@ -Format: http://dep.debian.net/deps/dep5 +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: librg-blast-parser-perl Upstream-Contact: Laszlo Kajan lka...@rostlab.org Source: http://rostlab.org/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r9989 - trunk/packages/gamgi/trunk
Author: alteholz Date: 2012-03-13 18:35:13 + (Tue, 13 Mar 2012) New Revision: 9989 Removed: trunk/packages/gamgi/trunk/debian/ Log: this package has been captured by debichem long time ago ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r9990 - trunk/packages/gamgi/trunk
Author: alteholz Date: 2012-03-13 18:35:50 + (Tue, 13 Mar 2012) New Revision: 9990 Added: trunk/packages/gamgi/trunk/README.status Log: gone to DebiChem Added: trunk/packages/gamgi/trunk/README.status === --- trunk/packages/gamgi/trunk/README.status(rev 0) +++ trunk/packages/gamgi/trunk/README.status2012-03-13 18:35:50 UTC (rev 9990) @@ -0,0 +1,7 @@ +--- +Format: 1 +Status: external +SVNDeleteRevision: 9989 +Comment: + Since 2009 this package is maintained within DebiChem. + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
