[med-svn] r7780 - in trunk/packages/wise/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Wed Sep 14 00:43:43 UTC 2011
Author: plessy
Date: 2011-09-14 00:43:42 +0000 (Wed, 14 Sep 2011)
New Revision: 7780
Added:
trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch
Modified:
trunk/packages/wise/trunk/debian/changelog
trunk/packages/wise/trunk/debian/patches/series
Log:
Correct src/models/makefile to link --as-needed.
This patch was extracted from the monolithic patch at
http://launchpadlibrarian.net/79698350/wise_2.4.1-8_2.4.1-8ubuntu1.diff.gz
where the changes for this issue were convoluted with changes
related to glib.
I am a bit demotivated by receiving big debdiffs instead of proper patches.
It is not because I am not payed that my time is less precious.
Modified: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog 2011-09-13 15:47:01 UTC (rev 7779)
+++ trunk/packages/wise/trunk/debian/changelog 2011-09-14 00:43:42 UTC (rev 7780)
@@ -1,3 +1,9 @@
+wise (2.4.1-9) UNRELEASED; urgency=low
+
+ * Correct src/models/makefile to link --as-needed (Closes: #641333).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 14 Sep 2011 09:38:06 +0900
+
wise (2.4.1-8) unstable; urgency=low
* Fixed conflicting definitions of getline(). (Closes: #552821)
Added: trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch (rev 0)
+++ trunk/packages/wise/trunk/debian/patches/07_ld--as-needed.patch 2011-09-14 00:43:42 UTC (rev 7780)
@@ -0,0 +1,54 @@
+Description: Fix FTBFS with ld --as-needed.
+Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
+
+diff --git a/src/models/makefile b/src/models/makefile
+index 1766fee..e4634b5 100644
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c
+ $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
+
+ scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread
++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LFLAGS)
+
+ scanwisep_compress.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
+@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o
+ $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
+
+ genewise : genewise.o $(NEWG)
+- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LFLAGS)
+
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o
+ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
+@@ -300,16 +300,16 @@ efgw : genewise.o $(NEWG)
+
+
+ genewisedb : genewisedb.o $(NEWG)
+- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LFLAGS)
+
+ estwisedb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LFLAGS)
+
+ edb : estwisedb.o $(NEWG)
+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence
+
+ estwise : estwise.o $(NEWG)
+- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LFLAGS)
+
+
+ amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o
+@@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
+ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
+
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG)
+- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LFLAGS)
+
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
Modified: trunk/packages/wise/trunk/debian/patches/series
===================================================================
--- trunk/packages/wise/trunk/debian/patches/series 2011-09-13 15:47:01 UTC (rev 7779)
+++ trunk/packages/wise/trunk/debian/patches/series 2011-09-14 00:43:42 UTC (rev 7780)
@@ -1,6 +1 @@
-01_welcome-csh.patch
-02_isnumber.patch
-03_doc-nodycache.patch
-04_wise2-pdflatex-update.patch
-05_glib2.patch
-06_getline.patch
+07_ld--as-needed.patch
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