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

[Andreas Tille]

Hi 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
> 
> 
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