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

[Sascha Steinbiss]

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
>> 
>> 
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