[med-svn] r8680 - in trunk/packages/autodock-vina/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-11-28 12:19:01 +0000 (Mon, 28 Nov 2011)
New Revision: 8680

Modified:
   trunk/packages/autodock-vina/trunk/debian/changelog
   trunk/packages/autodock-vina/trunk/debian/compat
   trunk/packages/autodock-vina/trunk/debian/control
   trunk/packages/autodock-vina/trunk/debian/patches/fix_boost.patch
Log:
Fixed build problems thanks to Sebastian Ramacher <s.ramacher at gmx.at>; usual packaging updates


Modified: trunk/packages/autodock-vina/trunk/debian/changelog
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/changelog	2011-11-28 10:28:16 UTC (rev 8679)
+++ trunk/packages/autodock-vina/trunk/debian/changelog	2011-11-28 12:19:01 UTC (rev 8680)
@@ -1,8 +1,10 @@
-autodock-vina (1.1.2-2) UNRELEASED; urgency=low
+autodock-vina (1.1.2-2) unstable; urgency=low
 
-  * Fix boost compatibility error
+  * Fix boost compatibility error (thanks for the patch to
+    Sebastian Ramacher <s.ramacher at gmx.at>)
     Closes: #642697
   * debian/control: Fixed Vcs fields
+  * Debhelper 8 (control+compat)
 
  -- Andreas Tille <tille at debian.org>  Mon, 28 Nov 2011 10:58:42 +0100
 

Modified: trunk/packages/autodock-vina/trunk/debian/compat
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/compat	2011-11-28 10:28:16 UTC (rev 8679)
+++ trunk/packages/autodock-vina/trunk/debian/compat	2011-11-28 12:19:01 UTC (rev 8680)
@@ -1 +1 @@
-7
+8

Modified: trunk/packages/autodock-vina/trunk/debian/control
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/control	2011-11-28 10:28:16 UTC (rev 8679)
+++ trunk/packages/autodock-vina/trunk/debian/control	2011-11-28 12:19:01 UTC (rev 8680)
@@ -7,7 +7,7 @@
  Yask Gupta <yask.gupta87 at gmail.com>,
  Michael Banck <mbanck at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7), libboost-all-dev
+Build-Depends: debhelper (>= 8), libboost-all-dev
 Standards-Version: 3.9.2
 Homepage: http://vina.scripps.edu
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/autodock-vina/trunk/

Modified: trunk/packages/autodock-vina/trunk/debian/patches/fix_boost.patch
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/patches/fix_boost.patch	2011-11-28 10:28:16 UTC (rev 8679)
+++ trunk/packages/autodock-vina/trunk/debian/patches/fix_boost.patch	2011-11-28 12:19:01 UTC (rev 8680)
@@ -1,5 +1,25 @@
+--- autodock-vina-1.1.2.orig/build/makefile_common
++++ autodock-vina-1.1.2/build/makefile_common
+@@ -10,7 +10,7 @@
+ 
+ LDFLAGS = -L$(BASE)/lib -L.
+ 
+-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
++LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION} -lboost_filesystem${BOOST_LIB_VERSION} #-l pthread
+ 
+ .SUFFIXES: .cpp .o
+ 
 --- autodock-vina-1.1.2.orig/src/main/main.cpp
 +++ autodock-vina-1.1.2/src/main/main.cpp
+@@ -47,7 +47,7 @@
+ using boost::filesystem::path;
+ 
+ path make_path(const std::string& str) {
+-	return path(str, boost::filesystem::native);
++	return path(str);
+ }
+ 
+ void doing(int verbosity, const std::string& str, tee& log) {
 @@ -661,7 +661,7 @@
  					cpu, seed, verbosity, max_modes_sz, energy_range, log);
  	}
@@ -18,3 +38,32 @@
  		return 1;
  	}
  	catch(std::bad_alloc&) {
+--- autodock-vina-1.1.2.orig/src/split/split.cpp
++++ autodock-vina-1.1.2/src/split/split.cpp
+@@ -38,7 +38,7 @@
+ using boost::filesystem::path;
+ 
+ path make_path(const std::string& str) {
+-	return path(str, boost::filesystem::native);
++	return path(str);
+ }
+ 
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,7 @@
+ 		write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ 	}
+ 	catch(file_error& e) {
+-		std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++		std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+ 		return 1;
+ 	}
+ 	catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +220,7 @@
+ 		return 1;
+ 	}
+ 	catch(parse_error& e) {
+-		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
+ 		return 1;
+ 	}
+ 	catch(std::bad_alloc&) {