[med-svn] r18002 - in trunk/packages/seg/trunk/debian: . patches
Laszlo Kajan
lkajan at moszumanska.debian.org
Sat Sep 13 19:11:56 UTC 2014
Author: lkajan
Date: 2014-09-13 19:11:56 +0000 (Sat, 13 Sep 2014)
New Revision: 18002
Added:
trunk/packages/seg/trunk/debian/patches/clang.patch
Modified:
trunk/packages/seg/trunk/debian/changelog
trunk/packages/seg/trunk/debian/control
trunk/packages/seg/trunk/debian/patches/series
Log:
fixes 'fails to build with clang instead of gcc'
Modified: trunk/packages/seg/trunk/debian/changelog
===================================================================
--- trunk/packages/seg/trunk/debian/changelog 2014-09-12 15:51:09 UTC (rev 18001)
+++ trunk/packages/seg/trunk/debian/changelog 2014-09-13 19:11:56 UTC (rev 18002)
@@ -1,3 +1,9 @@
+ncbi-seg (0.0.20000620-2) unstable; urgency=medium
+
+ * Fixes 'fails to build with clang instead of gcc' (Closes: #742060)
+
+ -- Laszlo Kajan <lkajan at debian.org> Sat, 13 Sep 2014 21:10:16 +0200
+
ncbi-seg (0.0.20000620-1) unstable; urgency=low
* Initial version. (Closes: #680233)
Modified: trunk/packages/seg/trunk/debian/control
===================================================================
--- trunk/packages/seg/trunk/debian/control 2014-09-12 15:51:09 UTC (rev 18001)
+++ trunk/packages/seg/trunk/debian/control 2014-09-13 19:11:56 UTC (rev 18002)
@@ -2,12 +2,11 @@
Section: science
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Uploaders: Laszlo Kajan <lkajan at debian.org>
Build-Depends: debhelper (>= 8), dh-autoreconf
-Standards-Version: 3.9.3
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seg/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seg/trunk/
-DM-Upload-Allowed: yes
+Standards-Version: 3.9.5
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seg/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seg/trunk/
Homepage: ftp://ftp.ncbi.nih.gov/pub/seg/seg/
Package: ncbi-seg
Added: trunk/packages/seg/trunk/debian/patches/clang.patch
===================================================================
--- trunk/packages/seg/trunk/debian/patches/clang.patch (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/clang.patch 2014-09-13 19:11:56 UTC (rev 18002)
@@ -0,0 +1,218 @@
+Description: make it compile with clang
+From: Nicolas Sévelin-Radiguet <nicosr at free.fr>
+
+--- a/seg.c
++++ b/seg.c
+@@ -130,7 +130,7 @@
+ downset = (window+1)/2 - 1;
+ upset = window - downset;
+
+- if (i==argc) return;
++ if (i==argc) return 0;
+
+ nargc = argc-i+1;
+ nargv = argv+(i-1);
+@@ -202,7 +202,7 @@
+ }
+ }
+
+- return;
++ return 0;
+ }
+
+ /*---------------------------------------------------------------(segment)---*/
+@@ -220,7 +220,7 @@
+ double *H, *seqent();
+
+ H = seqent(seq);
+- if (H==NULL) return;
++ if (H==NULL) return -1;
+
+ first = downset;
+ last = seq->length - upset;
+@@ -277,7 +277,7 @@
+ }
+
+ free(H);
+- return;
++ return 0;
+ }
+
+ /*----------------------------------------------------------------(seqent)---*/
+@@ -421,7 +421,7 @@
+ /* fprintf(stderr, "%d-%d\n", *leftend, *rightend); */
+
+ closewin(seq);
+- return;
++ return 0;
+ }
+
+ /*---------------------------------------------------------------(getprob)---*/
+@@ -511,8 +511,8 @@
+ {struct Segment *seg, *nextseg;
+ int len;
+
+- if (overlaps) return;
+- if (segs==NULL) return;
++ if (overlaps) return -1;
++ if (segs==NULL) return -1;
+
+ if (segs->begin<hilenmin) segs->begin = 0;
+
+@@ -545,7 +545,7 @@
+ len = seq->length - seg->end - 1;
+ if (len<hilenmin) seg->end = seq->length - 1;
+
+- return;
++ return 0;
+ }
+
+ /*----------------------------------------------------------------(report)---*/
+@@ -564,7 +564,7 @@
+ enton(seq);
+ seqout(seq, hi, 1, seq->length);
+ /* fputc('\n', stdout); -- for spacing after each sequence */
+- return;
++ return 0;
+ }
+
+ if (segs->begin>0)
+@@ -609,7 +609,7 @@
+ if (seg->end+1==seq->length)
+ {
+ /* fputc('\n', stdout); -- for spacing after each sequence */
+- return;
++ return 0;
+ }
+
+ subseq = openwin(seq, seg->end+1, seq->length-seg->end-1);
+@@ -618,7 +618,7 @@
+ closewin(subseq);
+
+ /* fputc('\n', stdout); -- for spacing after each sequence */
+- return;
++ return 0;
+ }
+
+ /*------------------------------------------------------------(singreport)---*/
+@@ -843,8 +843,8 @@
+ static int lo = 0;
+ int i, ctr, iend;
+
+- if (hionly && hilo==lo) return;
+- if (loonly && hilo==hi) return;
++ if (hionly && hilo==lo) return -1;
++ if (loonly && hilo==hi) return -1;
+
+ proseq = seq->seq;
+ proseqmax = proseq + seq->length;
+@@ -922,7 +922,7 @@
+ }
+ }
+
+- return;
++ return 0;
+ }
+
+ /*--------------------------------------------------------------(freesegs)---*/
+--- a/genwin.c
++++ b/genwin.c
+@@ -78,7 +78,7 @@
+ aaflag[c] = FALSE;
+ aaflag[tolower(c)] = FALSE;
+ }
+- return;
++ return 0;
+ }
+
+ /*-------------------------------------------------------------(opendbase)---*/
+@@ -150,7 +150,7 @@
+ free(dbase->indexname);
+ free(dbase);
+
+- return;
++ return 0;
+ }
+
+ /*--------------------------------------------------------------(firstseq)---*/
+@@ -186,7 +186,7 @@
+ struct Sequence *seq;
+
+ {
+- if (seq==NULL) return;
++ if (seq==NULL) return 0;
+
+ if (seq->id!=NULL) free(seq->id);
+ if (seq->name!=NULL) free(seq->name);
+@@ -196,7 +196,7 @@
+ if (seq->composition!=NULL) free(seq->composition);
+ free(seq->seq);
+ free(seq);
+- return;
++ return 0;
+ }
+
+ /*---------------------------------------------------------------(openwin)---*/
+@@ -320,7 +320,7 @@
+ struct Sequence *win;
+
+ {
+- if (win==NULL) return;
++ if (win==NULL) return 0;
+
+ if (win->state!=NULL) free(win->state);
+ if (win->composition!=NULL) free(win->composition);
+@@ -328,7 +328,7 @@
+ if (win->scorevec!=NULL) free(win->scorevec);
+
+ free(win);
+- return;
++ return 0;
+ }
+
+ /*----------------------------------------------------------------(compon)---*/
+@@ -350,7 +350,7 @@
+ comp[aaindex[aa]]++;
+ }
+
+- return;
++ return 0;
+ }
+
+ /*---------------------------------------------------------------(stateon)---*/
+@@ -381,7 +381,7 @@
+
+ qsort(win->state, nel, sizeof(win->state[0]), state_cmp);
+
+- return;
++ return 0;
+ }
+
+ /*-----------------------------------------------------------------(enton)---*/
+@@ -394,7 +394,7 @@
+
+ win->entropy = entropy(win->state);
+
+- return;
++ return 0;
+ }
+
+ /*---------------------------------------------------------------(entropy)---*/
+@@ -689,7 +689,7 @@
+ while ((c=getc(fp))!='\n' && c!=EOF)
+ ;
+
+- return;
++ return 0;
+ }
+
+ /*--------------------------------------------------------------(findchar)---*/
+@@ -787,7 +787,7 @@
+
+ seq->length = strlen(seq->seq);
+
+- return;
++ return 0;
+ }
+ /*-----------------------------------------------------------------(upper)---*/
+
Modified: trunk/packages/seg/trunk/debian/patches/series
===================================================================
--- trunk/packages/seg/trunk/debian/patches/series 2014-09-12 15:51:09 UTC (rev 18001)
+++ trunk/packages/seg/trunk/debian/patches/series 2014-09-13 19:11:56 UTC (rev 18002)
@@ -4,3 +4,4 @@
genwin.c
autotools
seg.pod
+clang.patch
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