I'm not sure if I should bother you team with this, apologies in case it's a bother. I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything seems to work just fine, except for mzR. Here is failed build: g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o rampR.o R_init_mzR.o -lpthread -lnetcdf -L/usr/lib64/R/lib -lR g++: error: cramp.o: No such file or directory g++: error: ramp_base64.o: No such file or directory g++: error: ramp.o: No such file or directory g++: error: RcppRamp.o: No such file or directory g++: error: RcppRampModule.o: No such file or directory g++: error: rnetCDF.o: No such file or directory g++: error: RcppPwiz.o: No such file or directory g++: error: RcppPwizModule.o: No such file or directory g++: error: RcppIdent.o: No such file or directory g++: error: RcppIdentModule.o: No such file or directory /usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' failed make: *** [mzR.so] Error 1 It did compile with 5.2.x (from devtoolset-4) and worked fine. I'm hoping you guys could confirm it is purely compiler problem? Or point me(not a real programmer) a way to troubleshoot it properly? many thanks, L.
mzR is a Bioconductor package, so better to ask on the Bioconductor support forum https://support.bioconductor.org Oh, I see you did, and then the advice is to avoid cross-posting! The missing .o files would have been produced in an earlier compilation step; they likely failed in some way, so you need to provide the complete compilation output. Did you do this on a version of the package that did not have any previous build artifacts (e.g., via biocLite() or from a fresh svn checkout)? Martin On 12/21/2016 12:00 PM, lejeczek via R-devel wrote:> I'm not sure if I should bother you team with this, apologies in case > it's a bother. > > I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything seems to > work just fine, except for mzR. > Here is failed build: > > g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o mzR.so cramp.o > ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o > RcppPwizModule.o RcppIdent.o RcppIdentModule.o > ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o > ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o > ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o > ./boost/regex/src/instances.o ./boost/regex/src/icu.o > ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o > ./boost/regex/src/wide_posix_api.o > ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o > ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o > ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o > ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o > ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o > ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o > ./boost/filesystem/src/path.o > ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o > ./boost/chrono/src/process_cpu_clocks.o > ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o > ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o > ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o > ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o > ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o > ./pwiz/data/msdata/DefaultReaderList.o > ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o > ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o > ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o > ./pwiz/data/msdata/Serializer_mzXML.o > ./pwiz/data/msdata/SpectrumList_mzML.o > ./pwiz/data/msdata/SpectrumList_MSn.o > ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o > ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o > ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o > ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o > ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o > ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o > ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o > ./pwiz/data/msdata/Index_mzML.o > ./pwiz/data/msdata/SpectrumWorkerThreads.o > ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o > ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o > ./pwiz/data/identdata/Serializer_protXML.o > ./pwiz/data/identdata/Serializer_pepXML.o > ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o > ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o > ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o > ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o > ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o > ./pwiz/utility/chemistry/Chemistry.o > ./pwiz/utility/chemistry/ChemistryData.o > ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o > ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o > ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o > ./pwiz/utility/misc/TabReader.o > ./pwiz/utility/misc/random_access_compressed_ifstream.o > ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o > ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o > rampR.o R_init_mzR.o -lpthread -lnetcdf -L/usr/lib64/R/lib -lR > g++: error: cramp.o: No such file or directory > g++: error: ramp_base64.o: No such file or directory > g++: error: ramp.o: No such file or directory > g++: error: RcppRamp.o: No such file or directory > g++: error: RcppRampModule.o: No such file or directory > g++: error: rnetCDF.o: No such file or directory > g++: error: RcppPwiz.o: No such file or directory > g++: error: RcppPwizModule.o: No such file or directory > g++: error: RcppIdent.o: No such file or directory > g++: error: RcppIdentModule.o: No such file or directory > /usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' failed > make: *** [mzR.so] Error 1 > > It did compile with 5.2.x (from devtoolset-4) and worked fine. > I'm hoping you guys could confirm it is purely compiler problem? Or > point me(not a real programmer) a way to troubleshoot it properly? > many thanks, > L. > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-develThis email message may contain legally privileged and/or...{{dropped:2}}
I do this on a vanilla-clean R installation, simply: > biocLite("mzR") it pulls some deps in which compile fine, only mzR fails. ... meanwhile... I grabbed devtools and comiled github master - still fails. Should I attach build log? One should not send attachments to the list.. I don't suppose? On 21/12/16 17:06, Martin Morgan wrote:> mzR is a Bioconductor package, so better to ask on the > Bioconductor support forum > > https://support.bioconductor.org > > Oh, I see you did, and then the advice is to avoid > cross-posting! > > The missing .o files would have been produced in an > earlier compilation step; they likely failed in some way, > so you need to provide the complete compilation output. > > Did you do this on a version of the package that did not > have any previous build artifacts (e.g., via biocLite() or > from a fresh svn checkout)? > > Martin > > On 12/21/2016 12:00 PM, lejeczek via R-devel wrote: >> I'm not sure if I should bother you team with this, >> apologies in case >> it's a bother. >> >> I'm trying gcc 6.2.1 (from devtoolset-6) with R, >> everything seems to >> work just fine, except for mzR. >> Here is failed build: >> >> g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o >> mzR.so cramp.o >> ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o >> rnetCDF.o RcppPwiz.o >> RcppPwizModule.o RcppIdent.o RcppIdentModule.o >> ./boost/system/src/error_code.o >> ./boost/regex/src/posix_api.o >> ./boost/regex/src/fileiter.o >> ./boost/regex/src/regex_raw_buffer.o >> ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o >> ./boost/regex/src/instances.o ./boost/regex/src/icu.o >> ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o >> ./boost/regex/src/wide_posix_api.o >> ./boost/regex/src/regex_traits_defaults.o >> ./boost/regex/src/winstances.o >> ./boost/regex/src/wc_regex_traits.o >> ./boost/regex/src/c_regex_traits.o >> ./boost/regex/src/cpp_regex_traits.o >> ./boost/regex/src/static_mutex.o >> ./boost/regex/src/w32_regex_traits.o >> ./boost/iostreams/src/zlib.o >> ./boost/iostreams/src/file_descriptor.o >> ./boost/thread/pthread/once.o >> ./boost/thread/pthread/thread.o >> ./boost/filesystem/src/operations.o >> ./boost/filesystem/src/path.o >> ./boost/filesystem/src/utf8_codecvt_facet.o >> ./boost/chrono/src/chrono.o >> ./boost/chrono/src/process_cpu_clocks.o >> ./boost/chrono/src/thread_clock.o >> ./pwiz/data/msdata/Version.o >> ./pwiz/data/common/MemoryIndex.o >> ./pwiz/data/common/CVTranslator.o >> ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o >> ./pwiz/data/common/BinaryIndexStream.o >> ./pwiz/data/common/diff_std.o >> ./pwiz/data/common/Unimod.o >> ./pwiz/data/msdata/SpectrumList_MGF.o >> ./pwiz/data/msdata/DefaultReaderList.o >> ./pwiz/data/msdata/ChromatogramList_mzML.o >> ./pwiz/data/msdata/examples.o >> ./pwiz/data/msdata/Serializer_mzML.o >> ./pwiz/data/msdata/Serializer_MSn.o >> ./pwiz/data/msdata/Reader.o >> ./pwiz/data/msdata/Serializer_MGF.o >> ./pwiz/data/msdata/Serializer_mzXML.o >> ./pwiz/data/msdata/SpectrumList_mzML.o >> ./pwiz/data/msdata/SpectrumList_MSn.o >> ./pwiz/data/msdata/BinaryDataEncoder.o >> ./pwiz/data/msdata/Diff.o >> ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o >> ./pwiz/data/msdata/SpectrumList_mzXML.o >> ./pwiz/data/msdata/IO.o >> ./pwiz/data/msdata/SpectrumList_BTDX.o >> ./pwiz/data/msdata/SpectrumInfo.o >> ./pwiz/data/msdata/RAMPAdapter.o >> ./pwiz/data/msdata/LegacyAdapter.o >> ./pwiz/data/msdata/SpectrumIterator.o >> ./pwiz/data/msdata/MSDataFile.o >> ./pwiz/data/msdata/MSNumpress.o >> ./pwiz/data/msdata/SpectrumListCache.o >> ./pwiz/data/msdata/Index_mzML.o >> ./pwiz/data/msdata/SpectrumWorkerThreads.o >> ./pwiz/data/identdata/IdentDataFile.o >> ./pwiz/data/identdata/IdentData.o >> ./pwiz/data/identdata/DefaultReaderList.o >> ./pwiz/data/identdata/Reader.o >> ./pwiz/data/identdata/Serializer_protXML.o >> ./pwiz/data/identdata/Serializer_pepXML.o >> ./pwiz/data/identdata/Serializer_mzid.o >> ./pwiz/data/identdata/IO.o >> ./pwiz/data/identdata/References.o >> ./pwiz/data/identdata/MascotReader.o >> ./pwiz/data/proteome/Modification.o >> ./pwiz/data/proteome/Digestion.o >> ./pwiz/data/proteome/Peptide.o >> ./pwiz/data/proteome/AminoAcid.o >> ./pwiz/utility/minimxml/XMLWriter.o >> ./pwiz/utility/minimxml/SAXParser.o >> ./pwiz/utility/chemistry/Chemistry.o >> ./pwiz/utility/chemistry/ChemistryData.o >> ./pwiz/utility/chemistry/MZTolerance.o >> ./pwiz/utility/misc/IntegerSet.o >> ./pwiz/utility/misc/Base64.o >> ./pwiz/utility/misc/IterationListener.o >> ./pwiz/utility/misc/MSIHandler.o >> ./pwiz/utility/misc/Filesystem.o >> ./pwiz/utility/misc/TabReader.o >> ./pwiz/utility/misc/random_access_compressed_ifstream.o >> ./pwiz/utility/misc/SHA1.o >> ./pwiz/utility/misc/SHA1Calculator.o >> ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o >> ./RcppExports.o >> rampR.o R_init_mzR.o -lpthread -lnetcdf >> -L/usr/lib64/R/lib -lR >> g++: error: cramp.o: No such file or directory >> g++: error: ramp_base64.o: No such file or directory >> g++: error: ramp.o: No such file or directory >> g++: error: RcppRamp.o: No such file or directory >> g++: error: RcppRampModule.o: No such file or directory >> g++: error: rnetCDF.o: No such file or directory >> g++: error: RcppPwiz.o: No such file or directory >> g++: error: RcppPwizModule.o: No such file or directory >> g++: error: RcppIdent.o: No such file or directory >> g++: error: RcppIdentModule.o: No such file or directory >> /usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' >> failed >> make: *** [mzR.so] Error 1 >> >> It did compile with 5.2.x (from devtoolset-4) and worked >> fine. >> I'm hoping you guys could confirm it is purely compiler >> problem? Or >> point me(not a real programmer) a way to troubleshoot it >> properly? >> many thanks, >> L. >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > > This email message may contain legally privileged and/or > confidential information. If you are not the intended > recipient(s), or the employee or agent responsible for the > delivery of this message to the intended recipient(s), you > are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. > If you have received this message in error, please notify > the sender immediately by e-mail and delete this email > message from your computer. Thank you.