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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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Make error #90

Closed Ruonan0101 closed 6 years ago

Ruonan0101 commented 6 years ago

Hi, There is some Make error at the end. At the source end of xerces, only 3.2.1 is found so I downloaded that. Can that be the potential cause of this? or something with WorkHorse.h? The attached is the log. make all-recursive make[1]: Entering directory /mnt/home/wuruona1/CRASS_meta_CRISPR/crass' Making all in src make[2]: Entering directory/mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src' Making all in aho-corasick make[3]: Entering directory /mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src/aho-corasick' /usr/bin/gcc -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -g -O2 -MT acism.o -MD -MP -MF .deps/acism.Tpo -c -o acism.o acism.c mv -f .deps/acism.Tpo .deps/acism.Po /usr/bin/gcc -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -g -O2 -MT acism_create.o -MD -MP -MF .deps/acism_create.Tpo -c -o acism_create.o acism_create.c mv -f .deps/acism_create.Tpo .deps/acism_create.Po /usr/bin/gcc -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -g -O2 -MT acism_dump.o -MD -MP -MF .deps/acism_dump.Tpo -c -o acism_dump.o acism_dump.c mv -f .deps/acism_dump.Tpo .deps/acism_dump.Po /usr/bin/gcc -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -g -O2 -MT acism_file.o -MD -MP -MF .deps/acism_file.Tpo -c -o acism_file.o acism_file.c mv -f .deps/acism_file.Tpo .deps/acism_file.Po /usr/bin/gcc -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -g -O2 -MT msutil.o -MD -MP -MF .deps/msutil.Tpo -c -o msutil.o msutil.c mv -f .deps/msutil.Tpo .deps/msutil.Po rm -f libacism.a ar cru libacism.a acism.o acism_create.o acism_dump.o acism_file.o msutil.o ranlib libacism.a make[3]: Leaving directory/mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src/aho-corasick' Making all in crass make[3]: Entering directory /mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src/crass' /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT PatternMatcher.o -MD -MP -MF .deps/PatternMatcher.Tpo -c -o PatternMatcher.o PatternMatcher.cpp mv -f .deps/PatternMatcher.Tpo .deps/PatternMatcher.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT Rainbow.o -MD -MP -MF .deps/Rainbow.Tpo -c -o Rainbow.o Rainbow.cpp mv -f .deps/Rainbow.Tpo .deps/Rainbow.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT LoggerSimp.o -MD -MP -MF .deps/LoggerSimp.Tpo -c -o LoggerSimp.o LoggerSimp.cpp mv -f .deps/LoggerSimp.Tpo .deps/LoggerSimp.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT SeqUtils.o -MD -MP -MF .deps/SeqUtils.Tpo -c -o SeqUtils.o SeqUtils.cpp mv -f .deps/SeqUtils.Tpo .deps/SeqUtils.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT CrisprNode.o -MD -MP -MF .deps/CrisprNode.Tpo -c -o CrisprNode.o CrisprNode.cpp mv -f .deps/CrisprNode.Tpo .deps/CrisprNode.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT NodeManager.o -MD -MP -MF .deps/NodeManager.Tpo -c -o NodeManager.o NodeManager.cpp mv -f .deps/NodeManager.Tpo .deps/NodeManager.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT libcrispr.o -MD -MP -MF .deps/libcrispr.Tpo -c -o libcrispr.o libcrispr.cpp libcrispr.cpp: In function ‘unsigned int extendPreRepeat(ReadHolder&, int, int)’: libcrispr.cpp:614: warning: comparison between signed and unsigned integer expressions libcrispr.cpp:756: warning: comparison between signed and unsigned integer expressions mv -f .deps/libcrispr.Tpo .deps/libcrispr.Po /usr/bin/g++ -DHAVE_CONFIG_H -I. -I../.. -I/opt/software/zlib/1.2.11--GCC-4.4.5/include -I/opt/software/boost/1.47.0--GCC-4.4.5/include -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include -I/opt/software/Python/2.7.2--GCC-4.4.5/include -I/opt/software/ClusterStudio/2011.0/composerxe-2011.5.220/tbb/include -I/opt/software/OpenMPI/1.4.3--GCC-4.4.5/include -I/usr/include -I/usr/include/xercesc -pedantic -Wall -g -O2 -MT WorkHorse.o -MD -MP -MF .deps/WorkHorse.Tpo -c -o WorkHorse.o WorkHorse.cpp WorkHorse.cpp: In member function ‘bool WorkHorse::addDataToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, int)’: WorkHorse.cpp:2049: error: ‘class xercesc_3_0::DOMElement’ has no member named ‘getFirstElementChild’ WorkHorse.cpp:2052: error: ‘class xercesc_3_0::DOMElement’ has no member named ‘getFirstElementChild’ WorkHorse.cpp:2052: error: ‘class xercesc_3_0::DOMElement’ has no member named ‘getNextElementSibling’ make[3]: *** [WorkHorse.o] Error 1 make[3]: Leaving directory/mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src/crass' make[2]: [all-recursive] Error 1 make[2]: Leaving directory `/mnt/home/wuruona1/CRASS_meta_CRISPR/crass/src' make[1]: [all-recursive] Error 1 make[1]: Leaving directory `/mnt/home/wuruona1/CRASS_meta_CRISPR/crass' make: *** [all] Error 2

ctSkennerton commented 6 years ago

I think this could be a version issue with xerces. Here is a link to the archive http://archive.apache.org/dist/xerces/c/3/sources/ Can you try with version 3.1.1

Ruonan0101 commented 6 years ago

Thanks. The installation is done.

ctSkennerton commented 6 years ago

great