Problems Installing Gkno

Question

[jftaylor]

Alright, So I have been attempting to install GKNO and am encountering the following build errors.

bamUtil.err

Validate.cpp:23:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
Convert.cpp:24:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
DumpHeader.cpp:23:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
In file included from Diff.cpp:23:0:
Diff.h:29:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
SplitChromosome.cpp:22:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
In file included from WriteRegion.cpp:22:0:
WriteRegion.h:26:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
ReadIndexedBam.cpp:24:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
DumpRefInfo.cpp:23:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
DumpIndex.cpp:23:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
Filter.cpp:24:21: fatal error: SamFile.h: No such file or directory
 #include "SamFile.h"
                     ^
compilation terminated.
In file included from GenomeSequence.h:47:0,
                 from Chromosome.h:4,
                 from Chromosome.cpp:2:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
cc1plus: all warnings being treated as errors
make[3]: *** [obj/Chromosome.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from GenomeSequence.h:47:0,
                 from GenomeSequence.cpp:25:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
make[1]: *** [../obj/Convert.o] Error 1
make[1]: *** Waiting for unfinished jobs....
cc1plus: all warnings being treated as errors
make[3]: *** [obj/GenomeSequence.o] Error 1
make[2]: *** [general] Error 2
make[1]: *** [../../libStatGen/libStatGen.a] Error 2
make[1]: *** [../obj/Validate.o] Error 1
make[1]: *** [../obj/DumpHeader.o] Error 1
make[1]: *** [../obj/WriteRegion.o] Error 1
make[1]: *** [../obj/SplitChromosome.o] Error 1
make[1]: *** [../obj/ReadIndexedBam.o] Error 1
make[1]: *** [../obj/DumpRefInfo.o] Error 1
make[1]: *** [../obj/Diff.o] Error 1
make[1]: *** [../obj/DumpIndex.o] Error 1
make[1]: *** [../obj/Filter.o] Error 1
In file included from ../../libStatGen/include/GenomeSequence.h:47:0,
                 from ReadReference.cpp:23:
../../libStatGen/include/GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
../../libStatGen/include/GenomeSequenceHelpers.h:67:44: warning: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
make: *** [src] Error 2

fastQValidator.err

FastQValidator.cpp:23:23: fatal error: FastQFile.h: No such file or directory
 #include "FastQFile.h"
                       ^
compilation terminated.
In file included from GenomeSequence.h:47:0,
                 from Chromosome.h:4,
                 from Chromosome.cpp:2:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
cc1plus: all warnings being treated as errors
make[3]: *** [obj/Chromosome.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[1]: *** [../obj/FastQValidator.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from GenomeSequence.h:47:0,
                 from GenomeSequence.cpp:25:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
cc1plus: all warnings being treated as errors
make[3]: *** [obj/GenomeSequence.o] Error 1
make[2]: *** [general] Error 2
make[1]: *** [../../libStatGen/libStatGen.a] Error 2
make: *** [src] Error 2

jellyfish.err

setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
---> bin
<--- bin
---> lib
---> lib/yaggo
<--- lib/yaggo
<--- lib
setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
---> bin
updating shebang: create_yaggo_one_file
updating shebang: yaggo
<--- bin
---> lib
---> lib/yaggo
<--- lib/yaggo
<--- lib
setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
rm -f InstalledFiles
---> bin
mkdir -p /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/bin
install create_yaggo_one_file /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/bin/
install yaggo /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/bin/
<--- bin
---> lib
mkdir -p /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib
---> lib/yaggo
mkdir -p /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install dsl.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install general.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install library.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install man_page.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install parser.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install stub.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install version.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install zsh_completion.rb /media/Storage1/Research/Applications/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
<--- lib/yaggo
<--- lib
configure.ac:8: error: possibly undefined macro: AC_PROG_LIBTOOL
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.
autoreconf: /usr/bin/autoconf failed with exit status: 1

libStatGen.err

In file included from GenomeSequence.h:47:0,
                 from Chromosome.h:4,
                 from Chromosome.cpp:2:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
cc1plus: all warnings being treated as errors
make[1]: *** [obj/Chromosome.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from GenomeSequence.h:47:0,
                 from GenomeSequence.cpp:25:
GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
         strncpy(species, newSpecies, sizeof(newSpecies));
                                            ^
cc1plus: all warnings being treated as errors
make[1]: *** [obj/GenomeSequence.o] Error 1
make: *** [general] Error 2

premo.err

*/gkno_launcher/tools/premo/src/libs/bamtools/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
*/gkno_launcher/tools/premo/src/libs/bamtools/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
                                                                                         ^
*/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
*/gkno_launcher/tools/premo/src/libs/bamtools/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
                                                                  ^
*/gkno_launcher/tools/premo/src/app/fastqreader.cpp: In member function ‘bool FastqReader::readNext(Fastq*)’:
*/gkno_launcher/tools/premo/src/app/fastqreader.cpp:219:11: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
     char* result;
           ^
*/gkno_launcher/tools/premo/src/app/premo.cpp: In function ‘void removeDirectory(std::string)’:
*/gkno_launcher/tools/premo/src/app/premo.cpp:200:28: error: ‘rmdir’ was not declared in this scope
     rmdir(directory.c_str());
                            ^
make[2]: *** [src/app/CMakeFiles/PremoApp.dir/premo.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/app/CMakeFiles/PremoApp.dir/all] Error 2
make: *** [all] Error 2

All programs can be installed on their own, outside of GKNO. Running Ubuntu 13.10 64-bit 3.11.0-15

[alistairnward]

Also, would you mind posting the gkno version? I have been trying to get a lot of major updates into gkno and the version has been changing regularly. I intend to have version 1.0.0 released this week.

Answer 1

[Michael]

SamFile.h is missing, that's why nothing won't compile, everything else is just a follow-up. Did you follow these instructions: http://blog.gkno.me/post/29962850248/getting-started-with-gkno