[Debian-med-packaging] Bug#812039: r21685 - in trunk/packages/proda/trunk/debian: . patches

[Andreas Tille]

Hi,

it now builds and I'll upload in a minute.

Thanks again for your work and sorry for the noise

      Andreas.

On Mon, Apr 11, 2016 at 08:59:26PM +0100, Sascha Steinbiss wrote:
> Hi Andreas,
> 
> did you get the latest commits? I added something afterwards to fix building on GCC5 again:
> 
> ------------------------------------------------------------------------
> r21688 | sascha-guest | 2016-04-11 19:43:00 +0000 (Mon, 11 Apr 2016) | 2 lines
> 
> add missing include, necessary for GCC <6
> 
> Cheers
> Sascha
> 
> 
> > thanks a lot for your bug squashing business.  Unfortunately the
> > package does not build for me:
> > 
> > ...
> > g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -lm AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAlign.o Main.o PairAligner.o Matrix.o MultiSequence.o ProbModel.o Score.o ScoreMatrix.o Sequence.o SparseMatrix.o Tree.o Utilities.o -o proda -Wl,-z,relro
> > /usr/bin/ld: errno: TLS definition in /lib/x86_64-linux-gnu/libc.so.6 section .tbss mismatches non-TLS reference in Main.o
> > /lib/x86_64-linux-gnu/libc.so.6: error adding symbols: Bad value
> > collect2: error: ld returned 1 exit status
> > 
> > Anything you might have forgotten to commit?
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > On Mon, Apr 11, 2016 at 07:22:30PM +0000, Sascha Steinbiss wrote:
> >> Author: sascha-guest
> >> Date: 2016-04-11 19:22:29 +0000 (Mon, 11 Apr 2016)
> >> New Revision: 21685
> >> 
> >> Added:
> >>   trunk/packages/proda/trunk/debian/patches/04-honour_CXX.patch
> >>   trunk/packages/proda/trunk/debian/patches/05-fix_FTBFS_with_GCC6.patch
> >> Modified:
> >>   trunk/packages/proda/trunk/debian/changelog
> >>   trunk/packages/proda/trunk/debian/patches/series
> >> Log:
> >> fix FTBFS
> >> 
> >> 
> >> Modified: trunk/packages/proda/trunk/debian/changelog
> >> ===================================================================
> >> --- trunk/packages/proda/trunk/debian/changelog	2016-04-11 18:55:13 UTC (rev 21684)
> >> +++ trunk/packages/proda/trunk/debian/changelog	2016-04-11 19:22:29 UTC (rev 21685)
> >> @@ -1,3 +1,10 @@
> >> +proda (1.0-9.1) unstable; urgency=medium
> >> +
> >> +  * Team upload.
> >> +  * Fix FTBFS with GCC-6. Closes #812039
> >> +
> >> + -- Sascha Steinbiss <sascha at steinbiss.name>  Mon, 11 Apr 2016 19:22:08 +0000
> >> +
> >> proda (1.0-9) unstable; urgency=low
> >> 
> >>   * debian/control: re-added David to uploaders, because he really
> >> 
> >> Added: trunk/packages/proda/trunk/debian/patches/04-honour_CXX.patch
> >> ===================================================================
> >> --- trunk/packages/proda/trunk/debian/patches/04-honour_CXX.patch	                        (rev 0)
> >> +++ trunk/packages/proda/trunk/debian/patches/04-honour_CXX.patch	2016-04-11 19:22:29 UTC (rev 21685)
> >> @@ -0,0 +1,24 @@
> >> +--- a/Makefile
> >> ++++ b/Makefile
> >> +@@ -6,7 +6,7 @@
> >> + # 1) Choose C++ compiler.
> >> + ################################################################################
> >> + 
> >> +-CXX = g++
> >> ++#CXX = g++
> >> + 
> >> + ################################################################################
> >> + # 2) Set C++ flags.
> >> +@@ -15,10 +15,10 @@
> >> + #    c) RELEASE mode
> >> + ################################################################################
> >> + 
> >> +-CPPFLAGS = -DVERSION="\"1.00\""
> >> ++CPPFLAGS+=-DVERSION="\"1.00\""
> >> + 
> >> + # debug mode    
> >> +-CXXFLAGS = -g -W -Wall -pedantic
> >> ++CXXFLAGS+=-g -W -Wall -pedantic
> >> + 
> >> + # profile mode
> >> + #CXXFLAGS = -pg -W -Wall -pedantic
> >> 
> >> Added: trunk/packages/proda/trunk/debian/patches/05-fix_FTBFS_with_GCC6.patch
> >> ===================================================================
> >> --- trunk/packages/proda/trunk/debian/patches/05-fix_FTBFS_with_GCC6.patch	                        (rev 0)
> >> +++ trunk/packages/proda/trunk/debian/patches/05-fix_FTBFS_with_GCC6.patch	2016-04-11 19:22:29 UTC (rev 21685)
> >> @@ -0,0 +1,11 @@
> >> +--- a/Main.cc
> >> ++++ b/Main.cc
> >> +@@ -117,7 +117,7 @@
> >> +   char *endPtr;
> >> +   long int retVal;
> >> + 
> >> +-  int errno = 0;
> >> ++  extern int errno;
> >> +   retVal = strtol (data, &endPtr, 0);
> >> +   if (retVal == 0 && (errno != 0 || data == endPtr)) return false;
> >> +   if (errno != 0 && (retVal == LONG_MAX || retVal == LONG_MIN)) return false;
> >> 
> >> Modified: trunk/packages/proda/trunk/debian/patches/series
> >> ===================================================================
> >> --- trunk/packages/proda/trunk/debian/patches/series	2016-04-11 18:55:13 UTC (rev 21684)
> >> +++ trunk/packages/proda/trunk/debian/patches/series	2016-04-11 19:22:29 UTC (rev 21685)
> >> @@ -1,4 +1,6 @@
> >> 01-fix_gcc4.3_warnings.patch
> >> 02-fix_CXXFLAGS.patch
> >> 03-fix_FTBFS_gcc4.3_missing_includes.patch
> >> +04-honour_CXX.patch
> >> +05-fix_FTBFS_with_GCC6.patch
> >> hardening.patch
> >> 
> >> 
> >> _______________________________________________
> >> debian-med-commit mailing list
> >> debian-med-commit at lists.alioth.debian.org
> >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
> >> 
> > 
> > -- 
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> 
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