Author: gert-guest Date: 2016-07-01 14:59:45 +0000 (Fri, 01 Jul 2016) New Revision: 22309
Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/gcc-6.patch Modified: trunk/packages/rostlab/disulfinder/trunk/debian/changelog trunk/packages/rostlab/disulfinder/trunk/debian/patches/series trunk/packages/rostlab/disulfinder/trunk/debian/rules Log: Correct compilation with gcc-6 and enable parallel builds Modified: trunk/packages/rostlab/disulfinder/trunk/debian/changelog =================================================================== --- trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2016-07-01 14:04:32 UTC (rev 22308) +++ trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2016-07-01 14:59:45 UTC (rev 22309) @@ -1,11 +1,17 @@ disulfinder (1.2.11-6) UNRELEASED; urgency=medium * Team upload. + + [Tatiana Malygina] * fix in install override in debian/rules * add harderning * add simple testsuite * cme fix dpkg-control * add README.test + + [Gert Wollny] + * d/p/gcc-6: Add patch to fix compilation with gcc-6, Closes: #811876 + * d/rules: enable parallel builds -- Tatiana Malygina <[email protected]> Sun, 26 Jun 2016 05:46:50 +0300 Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/gcc-6.patch =================================================================== --- trunk/packages/rostlab/disulfinder/trunk/debian/patches/gcc-6.patch (rev 0) +++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/gcc-6.patch 2016-07-01 14:59:45 UTC (rev 22309) @@ -0,0 +1,78 @@ +Description: compile with gcc-6 + This patch enables compiling with g++-6 (i.e. -std >= c++11) + Since the code uses their Assert function very often on iostream + objects, it was easier to make the Assert function actually accept + an iostream object instead of add .good() to each call. +Forwarded: no +Bug-Debian: http://bugs.debian.org/811876 +Author: Gert Wollny <[email protected]> +Last-Update: Fri, 1 Jul 2016 + +--- a/disulfind/src/Common/Exception.h ++++ b/disulfind/src/Common/Exception.h +@@ -3,6 +3,7 @@ + + #include <string> + #include <iostream> ++#include <stdarg.h> + using namespace std; + + //------------------------------------------------------------------------------------------------ +@@ -27,9 +28,35 @@ + static void Throw() { throw new Exception(); } + static void Throw(const string &mex) { throw new Exception(mex); } + static void Throw(const char *const format,...); ++ + static void Assert(bool condition) { if(!condition) throw new Exception(); } + static void Assert(bool condition, const char *const format,...); + static void Assert(bool condition, const string &mex) { if(!condition) throw new Exception(mex); } ++ ++#if __cplusplus >= 201103L ++ template<class CharT, class Traits = std::char_traits<CharT> > ++ static void Assert(const std::basic_ios<CharT,Traits>& stream) { ++ if(!stream) throw new Exception(); ++ } ++ ++ template<class CharT, class Traits = std::char_traits<CharT> > ++ static void Assert(const std::basic_ios<CharT,Traits>& stream, const char *const format,...) ++ { ++ va_list arglist; ++ if( !stream ) { ++ char mex[1000]; ++ va_start(arglist,format); ++ vsprintf(mex,format,arglist); ++ throw new Exception(mex); ++ } ++ } ++ ++ template<class CharT, class Traits = std::char_traits<CharT> > ++ static void Assert(const std::basic_ios<CharT,Traits>& stream, const string &mex) ++ { if(!stream) throw new Exception(mex); } ++#endif ++ ++ + }; + + #endif +--- a/disulfind/src/BRNN/rnn_util.cpp ++++ b/disulfind/src/BRNN/rnn_util.cpp +@@ -222,7 +222,7 @@ + // Read prediction and get bonded cystein indices + ifstream predfs(predfname.c_str()); + if(!predfs) { +- cerr << "create_connectivity_input_data: unable to open bonding state prediction file " << predfs << "\n"; ++ cerr << "create_connectivity_input_data: unable to open bonding state prediction file " << predfname << "\n"; + exit(1); + } + +--- a/disulfind/src/Common/Util.cpp ++++ b/disulfind/src/Common/Util.cpp +@@ -168,7 +168,7 @@ + string runCommand(string command) { + FILE *fp = popen(command.c_str(), "r"); + if( fp==NULL ) +- return false; ++ return ""; + + size_t read = 0; + char *buffer = NULL; Modified: trunk/packages/rostlab/disulfinder/trunk/debian/patches/series =================================================================== --- trunk/packages/rostlab/disulfinder/trunk/debian/patches/series 2016-07-01 14:04:32 UTC (rev 22308) +++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/series 2016-07-01 14:59:45 UTC (rev 22309) @@ -1,3 +1,4 @@ hardening.patch variable_length_array unknown_escape +gcc-6.patch Modified: trunk/packages/rostlab/disulfinder/trunk/debian/rules =================================================================== --- trunk/packages/rostlab/disulfinder/trunk/debian/rules 2016-07-01 14:04:32 UTC (rev 22308) +++ trunk/packages/rostlab/disulfinder/trunk/debian/rules 2016-07-01 14:59:45 UTC (rev 22309) @@ -9,7 +9,7 @@ pkgdata := $(pkg)-data %: - dh $@ + dh $@ --parallel override_dh_auto_install: $(MAKE) DESTDIR=$(CURDIR)/debian/$(pkg) prefix=/usr install _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
