[med-svn] r18516 - in trunk/packages/ncbi-blast+/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-11-25 17:44:08 +0000 (Tue, 25 Nov 2014)
New Revision: 18516

Added:
   trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation
Modified:
   trunk/packages/ncbi-blast+/trunk/debian/changelog
   trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
   trunk/packages/ncbi-blast+/trunk/debian/patches/series
   trunk/packages/ncbi-blast+/trunk/debian/rules
Log:
adapt patches to new release, add status to changelog

Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2014-11-24 13:30:11 UTC (rev 18515)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog	2014-11-25 17:44:08 UTC (rev 18516)
@@ -3,6 +3,8 @@
   * New upstream release
   * d/control: switch to Standards 3.9.6 
     [TODO] fix missing Makefile.flat
+    [ISSUE] problem at compilation:
+      /usr/bin/ld: blastp_app.o: undefined symbol «kBlastMinorVersion»
     [DONE] updates patches to new release
 
  -- Olivier Sallou <osallou at debian.org>  Fri, 21 Nov 2014 18:21:26 +0100

Added: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation	                        (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation	2014-11-25 17:44:08 UTC (rev 18516)
@@ -0,0 +1,11 @@
+--- a/c++/src/util/regexp/pcretest.c
++++ b/c++/src/util/regexp/pcretest.c
+@@ -250,7 +250,7 @@
+     /* Read the next line by normal means, prompting if the file is stdin. */
+ 
+       {
+-      if (f == stdin) printf(prompt);
++      if (f == stdin) printf("%s",prompt);
+       if (fgets((char *)here, rlen,  f) == NULL)
+         return (here == start)? NULL : start;
+       }

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps	2014-11-24 13:30:11 UTC (rev 18515)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps	2014-11-25 17:44:08 UTC (rev 18516)
@@ -336,7 +336,7 @@
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
  
-+DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++DLL_DLIB = id2 id1 ncbi_xreader \
 +           xobjmgr seq xutil xncbi
 +
  WATCHERS = vasilche

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series	2014-11-24 13:30:11 UTC (rev 18515)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series	2014-11-25 17:44:08 UTC (rev 18516)
@@ -6,3 +6,4 @@
 use_pie_for_apps
 skip_services_unit_test
 fix_configure
+fix_compilation

Modified: trunk/packages/ncbi-blast+/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules	2014-11-24 13:30:11 UTC (rev 18515)
+++ trunk/packages/ncbi-blast+/trunk/debian/rules	2014-11-25 17:44:08 UTC (rev 18516)
@@ -42,7 +42,8 @@
 
 override_dh_auto_build:
 	cd c++/BUILD/build  && \
-	    make -f Makefile.flat all_projects="$(proj)"
+	     make all_r
+#	    make -f Makefile.flat all_projects="$(proj)"
 
 override_dh_auto_test:
 	-dh_auto_test