[med-svn] r10247 - in trunk/packages/snap/trunk/debian: . bin patches
Andreas Tille
tille at alioth.debian.org
Mon Apr 2 12:52:43 UTC 2012
Author: tille
Date: 2012-04-02 12:52:42 +0000 (Mon, 02 Apr 2012)
New Revision: 10247
Added:
trunk/packages/snap/trunk/debian/bin/
trunk/packages/snap/trunk/debian/bin/snap
trunk/packages/snap/trunk/debian/patches/
trunk/packages/snap/trunk/debian/patches/series
trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch
Modified:
trunk/packages/snap/trunk/debian/README.Debian
trunk/packages/snap/trunk/debian/changelog
trunk/packages/snap/trunk/debian/rules
trunk/packages/snap/trunk/debian/snap.install
Log:
Commit uncommitted changes in patches; wrapper to set environment variable ZOE to implement hint given in 00README installation instructions --> removed the now useless hint in README.Debian
Modified: trunk/packages/snap/trunk/debian/README.Debian
===================================================================
--- trunk/packages/snap/trunk/debian/README.Debian 2012-04-02 12:45:36 UTC (rev 10246)
+++ trunk/packages/snap/trunk/debian/README.Debian 2012-04-02 12:52:42 UTC (rev 10247)
@@ -1,6 +1,4 @@
snap for Debian
---------------
-The HMM folder is placed in /usr/share/snap.
-
-- Steffen Moeller <moeller at debian.org> Fri, 17 Jun 2011 00:52:12 +0200
Added: trunk/packages/snap/trunk/debian/bin/snap
===================================================================
--- trunk/packages/snap/trunk/debian/bin/snap (rev 0)
+++ trunk/packages/snap/trunk/debian/bin/snap 2012-04-02 12:52:42 UTC (rev 10247)
@@ -0,0 +1,2 @@
+#!/bin/sh
+ZOE=/usr/share/snap/Zoe /usr/lib/snap/snap $@
Modified: trunk/packages/snap/trunk/debian/changelog
===================================================================
--- trunk/packages/snap/trunk/debian/changelog 2012-04-02 12:45:36 UTC (rev 10246)
+++ trunk/packages/snap/trunk/debian/changelog 2012-04-02 12:52:42 UTC (rev 10247)
@@ -2,7 +2,7 @@
* debian/upstream: Added citation information
* debian/copyright: DEP5 issues
- * debian/README.Debian: Removed informatiojn which is not intended
+ * debian/README.Debian: Removed information which is not intended
for users
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debhelper 9 (control+compat)
@@ -13,6 +13,8 @@
- Work around self-made build system and save original files
before configuration and restore these in clean target
- Use help2man to create simple man pages where possible
+ * debian/bin/snap: wrapper to set environment variable ZOE to implement
+ hint given in 00README installation instructions
-- Andreas Tille <tille at debian.org> Sun, 01 Apr 2012 18:40:17 +0200
Added: trunk/packages/snap/trunk/debian/patches/series
===================================================================
--- trunk/packages/snap/trunk/debian/patches/series (rev 0)
+++ trunk/packages/snap/trunk/debian/patches/series 2012-04-02 12:52:42 UTC (rev 10247)
@@ -0,0 +1 @@
+unused-but-set-variable.patch
Added: trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch
===================================================================
--- trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch (rev 0)
+++ trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch 2012-04-02 12:52:42 UTC (rev 10247)
@@ -0,0 +1,96 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Sun, 01 Apr 2012 18:40:17 +0200
+Description: When enabling hardening flags by
+ using debhelper 9 unsused variables should not be assigned.
+ This patch comments those variables.
+
+--- snap-2010-07-28.orig/Zoe/zoeAlignment.c
++++ snap-2010-07-28/Zoe/zoeAlignment.c
+@@ -720,15 +720,15 @@
+ zoeVec zoeChainHSPs (const zoeVec HSPs) {
+ int i;
+ zoeVec bestHSPs = NULL; /* shush */
+- zoeVec qvec;
+- zoeVec svec;
++ /* zoeVec qvec; */
++ /* zoeVec svec; */
+
+ for (i = 0; i < HSPs->size; i++) {
+ zoeWriteHSP(stdout, HSPs->elem[i]);
+ }
+
+- qvec = zoeGroupHSPs(HSPs, 'q');
+- svec = zoeGroupHSPs(HSPs, 's');
++ /* qvec = */ zoeGroupHSPs(HSPs, 'q');
++ /* svec = */ zoeGroupHSPs(HSPs, 's');
+
+ return bestHSPs;
+ }
+--- snap-2010-07-28.orig/Zoe/zoeCDS.c
++++ snap-2010-07-28/Zoe/zoeCDS.c
+@@ -396,7 +396,7 @@
+ char text[256];
+ struct exon_feature efstart, efstop;
+ struct best_translation bt;
+- int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, all_exon, split;
++ int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, /* all_exon, */ split;
+ int exstart, exend, exinc;
+
+ /* assigned immediately */
+@@ -483,10 +483,10 @@
+ }
+
+ /* re-label generic exons as Einit, Eterm, Esngl only if all exons defined as Exon */
+- all_exon = 1;
++ /* all_exon = 1; */
+ for (i = 0; i < cds->exons->size; i++) {
+ if (cds->exons->elem[i]->label != Exon) {
+- all_exon = 0;
++ /* all_exon = 0; */
+ break;
+ }
+ }
+--- snap-2010-07-28.orig/Zoe/zoeFeature.c
++++ snap-2010-07-28/Zoe/zoeFeature.c
+@@ -167,7 +167,7 @@
+ zoeFeature zoeReadGFF (FILE * stream) {
+ char line[1024], Source[64], ID[64], Label[64],
+ Start[16], End[16], Strand[8], Score[32], Frame[8], Group[512];
+- char * group = NULL;
++ /* char * group = NULL; */
+ zoeLabel label;
+ coor_t start, end;
+ strand_t strand;
+@@ -178,10 +178,10 @@
+
+ if (sscanf(line, "%s %s %s %s %s %s %s %s %s", /* group */
+ Source, ID, Label, Start, End, Score, Strand, Frame, Group) == 9) {
+- group = Group;
++ /* group = Group */ ;
+ } else if (sscanf(line, "%s %s %s %s %s %s %s %s", /* no group */
+ Source, ID, Label, Start, End, Score, Strand, Frame) == 8) {
+- group = NULL;
++ /* group = NULL */ ;
+ } else {
+ zoeWarn("zoeReadGFF format not valid");
+ return NULL;
+--- snap-2010-07-28.orig/Zoe/zoeFeatureFactory.c
++++ snap-2010-07-28/Zoe/zoeFeatureFactory.c
+@@ -280,7 +280,7 @@
+ int f0, f1, f2;
+ int * fstop;
+ coor_t i;
+- int frame; /* should be frame_t, but screw casting */
++ /* int frame; *//* should be frame_t, but screw casting */
+ zoeDNA dna = cds_scan->dna;
+ zoeFeatureFactory factory = zoeMalloc(sizeof(struct zoeFeatureFactory));
+
+@@ -334,7 +334,7 @@
+ fstop[2] = 2;
+
+ for (i = 3; i < dna->length; i++) {
+- frame = i % 3;
++ /* frame = i % 3; */
+ if (stop[i] != MIN_SCORE) {
+ fstop[i] = i;
+ } else {
Modified: trunk/packages/snap/trunk/debian/rules
===================================================================
--- trunk/packages/snap/trunk/debian/rules 2012-04-02 12:45:36 UTC (rev 10246)
+++ trunk/packages/snap/trunk/debian/rules 2012-04-02 12:52:42 UTC (rev 10247)
@@ -7,6 +7,7 @@
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/
bindir=$(CURDIR)/debian/$(pkg)/usr/bin
+libdir=$(CURDIR)/debian/$(pkg)/usr/lib/snap
version=$(shell dpkg-parsechangelog | grep '^Version:' | sed 's/^Version: \(.*\)-[^-]\+$$/\1/')
%:
@@ -28,7 +29,7 @@
help2man --no-info --no-discard-stderr -h "" \
--version-string="$(version)" \
--name="Semi-HMM-based Nucleic Acid Parser" \
- $(bindir)/snap > $(mandir)/snap.1
+ $(libdir)/snap > $(mandir)/snap.1
help2man --no-info --no-discard-stderr -h "" \
--version-string="$(version)" \
$(bindir)/exonpairs > $(mandir)/exonpairs.1
Modified: trunk/packages/snap/trunk/debian/snap.install
===================================================================
--- trunk/packages/snap/trunk/debian/snap.install 2012-04-02 12:45:36 UTC (rev 10246)
+++ trunk/packages/snap/trunk/debian/snap.install 2012-04-02 12:52:42 UTC (rev 10247)
@@ -1,13 +1,14 @@
exonpairs usr/bin
hmm-info usr/bin
-forge usr/bin
-fathom usr/bin
-snap usr/bin
+forge usr/bin
+fathom usr/bin
+snap usr/lib/snap
+debian/bin/snap usr/bin
cds-trainer.pl usr/bin
hmm-assembler.pl usr/bin
noncoding-trainer.pl usr/bin
patch-hmm.pl usr/bin
zff2gff3.pl usr/bin
-HMM usr/share/snap
+HMM usr/share/snap
Zoe/zoe-loop usr/bin
Zoe/blosum62 usr/share/snap/Zoe
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