[Debian-med-packaging] Bug#486959: fixed in proda 1.0-6

Lucas Nussbaum lucas at lucas-nussbaum.net
Thu Jul 3 10:15:33 UTC 2008 

reopen 486959
found 486959 1.0-6
thanks

>    * debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch:
>      Added `include <cstdio>' to `AlignedFragment.h' (Closes: #486959).

Apparently this wasn't enough. It seems that you start building before
patching. Sounds like a missing dependancy in debian/rules.

dh_clean build-stamp proda
[ ! -f Makefile ] || /usr/bin/make clean
make[1]: Entering directory `/build/user-proda_1.0-6-amd64-l9kwh7/proda-1.0-6'
rm -f *.o
make[1]: Leaving directory `/build/user-proda_1.0-6-amd64-l9kwh7/proda-1.0-6'
 dpkg-source -b proda-1.0-6
dpkg-source: warning: source directory 'proda-1.0-6' is not <sourcepackage>-<upstreamversion> 'proda-1.0'
dpkg-source: warning: .orig directory name proda-1.0-6.orig is not <package>-<upstreamversion> (wanted proda-1.0.orig)
dpkg-source: info: using source format `1.0'
dpkg-source: info: building proda using existing proda_1.0.orig.tar.gz
dpkg-source: info: building proda in proda_1.0-6.diff.gz
dpkg-source: info: building proda in proda_1.0-6.dsc
 debian/rules build
# quilt exits with 2 as return when there was nothing to do. 
dh_testdir
# That's not an error here (but it's useful to break loops in crude scripts)
QUILT_PATCHES=debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
/usr/bin/make CXXFLAGS="-Wall -g -O2"  --jobserver-fds=4,5 -j
make[1]: Entering directory `/build/user-proda_1.0-6-amd64-l9kwh7/proda-1.0-6'
g++ -Wall -g -O2   -c -o AlignedFragment.o AlignedFragment.cc
g++ -Wall -g -O2   -c -o Assert.o Assert.cc
g++ -Wall -g -O2   -c -o Block.o Block.cc
g++ -Wall -g -O2   -c -o Consistency.o Consistency.cc
g++ -Wall -g -O2   -c -o GlobalAlign.o GlobalAlign.cc
g++ -Wall -g -O2   -c -o LocalAlign.o LocalAlign.cc
g++ -Wall -g -O2   -c -o Main.o Main.cc
g++ -Wall -g -O2   -c -o PairAligner.o PairAligner.cc
In file included from AlignedFragment.cc:5:
AlignedFragment.h:21: error: 'FILE' has not been declared
AlignedFragment.cc: In constructor 'AlignedFragment::AlignedFragment(int, int, int, int, int, int, int*, int*)':
AlignedFragment.cc:40: warning: deprecated conversion from string constant to 'char*'
AlignedFragment.cc: In copy constructor 'AlignedFragment::AlignedFragment(const AlignedFragment&)':
AlignedFragment.cc:57: warning: deprecated conversion from string constant to 'char*'
AlignedFragment.cc: In member function 'AlignedFragment& AlignedFragment::operator=(AlignedFragment)':
AlignedFragment.cc:74: warning: deprecated conversion from string constant to 'char*'
AlignedFragment.cc: In member function 'void AlignedFragment::Adjust(Fragment&, Fragment&, AlignedFragment&, AlignedFragment&)':
AlignedFragment.cc:127: warning: deprecated conversion from string constant to 'char*'
AlignedFragment.cc:128: warning: deprecated conversion from string constant to 'char*'
AlignedFragment.cc: In member function 'void AlignedFragment::Prune()':
AlignedFragment.cc:190: error: 'memcpy' was not declared in this scope
AlignedFragment.cc: In member function 'int AlignedFragment::ProcessRepeat(AVECT&, int)':
AlignedFragment.cc:242: error: no matching function for call to 'AlignedFragment::Print(_IO_FILE*&)'
AlignedFragment.h:21: note: candidates are: void AlignedFragment::Print(int*)
AlignedFragment.cc:249: error: no matching function for call to 'AlignedFragment::Print(_IO_FILE*&)'
AlignedFragment.h:21: note: candidates are: void AlignedFragment::Print(int*)
AlignedFragment.cc: At global scope:
AlignedFragment.cc:271: error: prototype for 'void AlignedFragment::Print(FILE*)' does not match any in class 'AlignedFragment'
AlignedFragment.h:21: error: candidate is: void AlignedFragment::Print(int*)
make[1]: *** [AlignedFragment.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from Types.h:12,
                 from Block.h:10,
                 from Block.cc:5:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
Block.cc: In constructor 'Block::Block(std::vector<AlignedFragment, std::allocator<AlignedFragment> >&, MultiSequence*, bool, Block*)':
Block.cc:144: error: 'abs' was not declared in this scope
Block.cc:162: error: 'abs' was not declared in this scope
make[1]: *** [Block.o] Error 1
In file included from SparseMatrix.h:12,
                 from Consistency.h:10,
                 from Consistency.cc:5:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
Consistency.cc: In function 'SparseMatrix** ProbabilisticConsistency(SparseMatrix**, int)':
Consistency.cc:34: warning: deprecated conversion from string constant to 'char*'
In file included from GlobalAlign.h:11,
                 from GlobalAlign.cc:7:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
In file included from LocalAlign.h:12,
                 from LocalAlign.cc:5:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)':
LocalAlign.cc:17: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:20: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:24: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:25: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:79: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:87: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:96: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:98: warning: deprecated conversion from string constant to 'char*'
LocalAlign.cc:100: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc: In static member function 'static char* GlobalAlign::ComputeMWTrace(const Matrix&, float*, int*)':
GlobalAlign.cc:22: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc:25: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc:59: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc:66: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc:74: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc: In static member function 'static Sequence* GlobalAlign::InsertGaps(const Sequence&, const char*, char)':
GlobalAlign.cc:93: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc:96: warning: deprecated conversion from string constant to 'char*'
GlobalAlign.cc: In static member function 'static MultiSequence* GlobalAlign::BuildAlignment(const MultiSequence&, const MultiSequence&, const char*)':
GlobalAlign.cc:122: warning: deprecated conversion from string constant to 'char*'
In file included from Types.h:12,
                 from Block.h:10,
                 from MultiSequence.h:13,
                 from Main.cc:10:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
In file included from Sequence.h:11,
                 from PairAligner.h:10,
                 from PairAligner.cc:7:
AlignedFragment.h:21: error: 'FILE' has not been declared
In file included from PairAligner.h:10,
                 from PairAligner.cc:7:
Sequence.h:32: error: 'FILE' has not been declared
Main.cc: In function 'int main(int, char**)':
Main.cc:60: warning: deprecated conversion from string constant to 'char*'
Main.cc: In function 'bool GetInteger(char*, int*)':
Main.cc:122: error: 'LONG_MAX' was not declared in this scope
Main.cc:122: error: 'LONG_MIN' was not declared in this scope
Main.cc:123: error: 'INT_MIN' was not declared in this scope
Main.cc:123: error: 'INT_MAX' was not declared in this scope
Main.cc: In function 'void RunEM(ProbModel&, int, char**)':
Main.cc:140: warning: deprecated conversion from string constant to 'char*'
Main.cc:144: warning: deprecated conversion from string constant to 'char*'
Main.cc: In function 'void RunLocalAligner(int, char**)':
Main.cc:179: warning: deprecated conversion from string constant to 'char*'
Main.cc:187: warning: deprecated conversion from string constant to 'char*'
Main.cc:272: warning: deprecated conversion from string constant to 'char*'
In file included from Types.h:12,
                 from ProbModel.h:11,
                 from PairAligner.h:11,
                 from PairAligner.cc:7:
Matrix.h: In member function 'float& Matrix::operator()(int, int, int)':
Matrix.h:63: warning: deprecated conversion from string constant to 'char*'
Matrix.h:64: warning: deprecated conversion from string constant to 'char*'
Matrix.h:65: warning: deprecated conversion from string constant to 'char*'
Matrix.h: In member function 'const float& Matrix::operator()(int, int, int) const':
Matrix.h:74: warning: deprecated conversion from string constant to 'char*'
Matrix.h:75: warning: deprecated conversion from string constant to 'char*'
Matrix.h:76: warning: deprecated conversion from string constant to 'char*'
PairAligner.cc: In constructor 'PairAligner::PairAligner(ProbModel*, Sequence*, Sequence*)':
PairAligner.cc:23: warning: deprecated conversion from string constant to 'char*'
PairAligner.cc:24: error: 'memset' was not declared in this scope
PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)':
PairAligner.cc:74: error: 'abs' was not declared in this scope
make[1]: *** [Main.o] Error 1
PairAligner.cc:168: warning: deprecated conversion from string constant to 'char*'
PairAligner.cc:169: error: 'memset' was not declared in this scope
PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)':
PairAligner.cc:239: error: no matching function for call to 'AlignedFragment::Print(_IO_FILE*&)'
AlignedFragment.h:21: note: candidates are: void AlignedFragment::Print(int*)
PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)':
PairAligner.cc:318: error: no matching function for call to 'AlignedFragment::Print(_IO_FILE*&)'
AlignedFragment.h:21: note: candidates are: void AlignedFragment::Print(int*)
make[1]: *** [PairAligner.o] Error 1
Applying patch 01-fix_gcc4.3_warnings.patch
patching file Assert.cc
patching file Assert.h
patching file MultiSequence.cc
patching file ProbModel.cc

Applying patch 02-fix_CXXFLAGS.patch
patching file Makefile

Applying patch 03-fix_FTBFS_gcc4.3_missing_includes.patch
patching file AlignedFragment.cc
patching file AlignedFragment.h
patching file Block.cc
patching file Main.cc
patching file PairAligner.cc
patching file ProbModel.cc

make[1]: Leaving directory `/build/user-proda_1.0-6-amd64-l9kwh7/proda-1.0-6'
make: *** [build-stamp] Error 2
make: *** Waiting for unfinished jobs....
Now at patch 03-fix_FTBFS_gcc4.3_missing_includes.patch
touch debian/stamp-patched
dpkg-buildpackage: failure: debian/rules build gave error exit status 2
-- 
| Lucas Nussbaum
| lucas at lucas-nussbaum.net   http://www.lucas-nussbaum.net/ |
| jabber: lucas at nussbaum.fr             GPG: 1024D/023B3F4F |

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