Release tarball 0.3.0 doesn't compile

[andreas-wilm]

Downloaded the release (from github; i.e. not repo cloned) and tried to compile, but certain headers are missing (see below). Make modules doesn't work either because the release is not a git repository. Cloning the repo, then git checkout v0.3.0 and make modules; make works fine.

Might be worthwhile mentioning that the github created release tarball is broken and shouldn't be used

Andreas

GCC=/opt/gcc-4.7.2/bin/gcc make -j 4
mkdir -p obj_linux/src/alignment/
/opt/gcc-4.7.2/bin/gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"  -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment.o src/alignment/alignment.cc
mkdir -p obj_linux/src/alignment/
/opt/gcc-4.7.2/bin/gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"  -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
mkdir -p obj_linux/src/alignment/
/opt/gcc-4.7.2/bin/gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"  -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/anchored.o src/alignment/anchored.cc
mkdir -p obj_linux/src/alignment/
/opt/gcc-4.7.2/bin/gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"  -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/cigargen.o src/alignment/cigargen.cc
In file included from src/alignment/anchored.cc:8:0:
./src/alignment/alignment_wrappers.h:19:37: fatal error: utility/utility_general.h: No such file or directory
compilation terminated.
make: *** [obj_linux/src/alignment/anchored.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from src/alignment/alignment.cc:8:0:
./src/alignment/alignment.h:19:39: fatal error: sequences/single_sequence.h: No such file or directory
compilation terminated.
In file included from src/alignment/alignment_wrappers.cc:8:0:
src/alignment/alignment_wrappers.h:19:37: fatal error: utility/utility_general.h: No such file or directory
compilation terminated.
make: *** [obj_linux/src/alignment/alignment.o] Error 1
make: *** [obj_linux/src/alignment/alignment_wrappers.o] Error 1
In file included from src/alignment/cigargen.cc:8:0:
./src/alignment/cigargen.h:19:24: fatal error: libs/edlib.h: No such file or directory
compilation terminated.
make: *** [obj_linux/src/alignment/cigargen.o] Error 1

[VGalata]

Using the above suggestion, i.e. cloning the repository and checking out v0.3.0, produced in my case an error when running make (after make modules) for target obj_linux/src/alignment/alignment_wrappers.o.

Running make modules and make on latest version (eb8c75d) worked.

Error message:

src/alignment/alignment_wrappers.cc: In function ‘int LocalizeAlignmentPosWithMyers(const int8_t*, int64_t, const int8_t*, int64_t, int64_t, int64_t, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, bool)’:
src/alignment/alignment_wrappers.cc:44:70: error: ‘edlibCalcEditDistance’ was not declared in this scope
                         &current_alignment, &current_alignment_length);
                                                                      ^
src/alignment/alignment_wrappers.cc: In function ‘int MyersSemiglobalWrapper(const int8_t*, int64_t, const int8_t*, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t*, int64_t*, int64_t*, std::vector<unsigned char>&)’:
src/alignment/alignment_wrappers.cc:548:64: error: ‘edlibCalcEditDistance’ was not declared in this scope
                         &alignment, &alignment_length, &found_k);
                                                                ^
src/alignment/alignment_wrappers.cc: In function ‘int MyersNWWrapper(const int8_t*, int64_t, const int8_t*, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t*, int64_t*, int64_t*, std::vector<unsigned char>&)’:
src/alignment/alignment_wrappers.cc:601:64: error: ‘edlibCalcEditDistance’ was not declared in this scope
                         &alignment, &alignment_length, &found_k);
                                                                ^
src/alignment/alignment_wrappers.cc: In function ‘int MyersSHWWrapper(const int8_t*, int64_t, const int8_t*, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t, int64_t*, int64_t*, int64_t*, std::vector<unsigned char>&)’:
src/alignment/alignment_wrappers.cc:868:90: error: ‘edlibCalcEditDistance’ was not declared in this scope
                                                   &alignment, &alignment_length, &found_k);
                                                                                          ^
src/alignment/alignment_wrappers.cc:890:90: error: ‘edlibCalcEditDistance’ was not declared in this scope
                                                   &alignment, &alignment_length, &found_k);
                                                                                          ^
src/alignment/alignment_wrappers.cc: In function ‘int MyersEditDistanceWrapper(const int8_t*, int64_t, const int8_t*, int64_t, int64_t*, int64_t*, int)’:
src/alignment/alignment_wrappers.cc:963:66: error: ‘edlibCalcEditDistance’ was not declared in this scope
                           &alignment, &alignment_length, &found_k);

[abayega]

Thanks VGalata, that worked for me as well