hi guys, just an admin here. I wonder if anybody see what I see, or similar? I'm on Centos 7.x and this occurs with R 3.4.x 3.5.x and probably earlier versions too. Every time I use something like -j>1 to pass to a compiler, eg.echo -ne $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" | /usr/bin/R --vanilla mzR fails to compile: ... g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ -lnetcdf -L/usr/lib64/R/lib -lR g++: error: cramp.o: No such file or directory make: *** [mzR.so] Error 1 ERROR: compilation failed for package ?mzR? * removing ?/usr/lib64/R/library/mzR? If j is 1, then compilation succeeds. I have hundreds of packages and so far only "mzR" and "MSnbase" fail if I compile with -j>1. Would anybody be able to confirm this problem exists? Many thanks, L.
This is almost certainly a Makefile error. Something (A) is relying on something (B) without stating the dependency explicitly in the Makefile. You can get away with that (sometimes) in a non-parallel make, because the sequence of compilations is such that B gets built before A. However, with a parallel make, one thread may try to build A before B gets built by another thread. The fix is to add the dependency in the Makefile (plus any other issues of the same kind). In this case, AFAICT, you need mzR.so: cramp.o in addition to what might be there already and any other stuff that is also missing. If there is already something like mzR.so: $(OBJECTS) chances are that there is a deficient macro definition earlier on, so that cramp.o is not contained in OBJECTS. -pd> On 15 Jun 2018, at 16:49 , lejeczek via R-help <r-help at r-project.org> wrote: > > hi guys, just an admin here. > > I wonder if anybody see what I see, or similar? I'm on Centos 7.x and this occurs with R 3.4.x 3.5.x and probably earlier versions too. > > Every time I use something like -j>1 to pass to a compiler, eg.echo -ne > > $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" | /usr/bin/R --vanilla > > mzR fails to compile: > ... > g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ -lnetcdf -L/usr/lib64/R/lib -lR > g++: error: cramp.o: No such file or directory > make: *** [mzR.so] Error 1 > ERROR: compilation failed for package ?mzR? > * removing ?/usr/lib64/R/library/mzR? > > If j is 1, then compilation succeeds. > I have hundreds of packages and so far only "mzR" and "MSnbase" fail if I compile with -j>1. > > Would anybody be able to confirm this problem exists? > Many thanks, L. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
mzR is a Bioconductor package so you might have more luck contacting the maintainer on the Bioconductor support site https://support.bioconductor.org or on the 'bioc-devel' mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel or most directly by opening an issue on the maintainer's github https://github.com/sneumann/mzR/issues/ this is linked to from the package 'landing page' https://bioconductor.org/packages/mzR Martin Morgan On 06/15/2018 10:49 AM, lejeczek via R-help wrote:> hi guys, just an admin here. > > I wonder if anybody see what I see, or similar? I'm on Centos 7.x and > this occurs with R 3.4.x 3.5.x and probably earlier versions too. > > Every time I use something like -j>1 to pass to a compiler, eg.echo -ne > > $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n > source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"), > suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" | > /usr/bin/R --vanilla > > mzR fails to compile: > ... > g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o > ./boost/libs/regex/src/fileiter.o > ./boost/libs/regex/src/regex_raw_buffer.o > ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o > ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o > ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o > ./boost/libs/regex/src/wide_posix_api.o > ./boost/libs/regex/src/regex_traits_defaults.o > ./boost/libs/regex/src/winstances.o > ./boost/libs/regex/src/wc_regex_traits.o > ./boost/libs/regex/src/c_regex_traits.o > ./boost/libs/regex/src/cpp_regex_traits.o > ./boost/libs/regex/src/static_mutex.o > ./boost/libs/regex/src/w32_regex_traits.o > ./boost/libs/iostreams/src/zlib.o > ./boost/libs/iostreams/src/file_descriptor.o > ./boost/libs/filesystem/src/operations.o > ./boost/libs/filesystem/src/path.o > ./boost/libs/filesystem/src/utf8_codecvt_facet.o > ./boost/libs/chrono/src/chrono.o > ./boost/libs/chrono/src/process_cpu_clocks.o > ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o > ./pwiz/data/identdata/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/mz5/Configuration_mz5.o > ./pwiz/data/msdata/mz5/Connection_mz5.o > ./pwiz/data/msdata/mz5/Datastructures_mz5.o > ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o > ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o > ./pwiz/data/msdata/mz5/Translator_mz5.o > ./pwiz/data/msdata/SpectrumList_MGF.o > ./pwiz/data/msdata/DefaultReaderList.o > ./pwiz/data/msdata/ChromatogramList_mzML.o > ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 > ./boost/libs/thread/src/pthread/once.o > ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread > /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a > /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a > /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ > -lnetcdf -L/usr/lib64/R/lib -lR > g++: error: cramp.o: No such file or directory > make: *** [mzR.so] Error 1 > ERROR: compilation failed for package ?mzR? > * removing ?/usr/lib64/R/library/mzR? > > If j is 1, then compilation succeeds. > I have hundreds of packages and so far only "mzR" and "MSnbase" fail if > I compile with -j>1. > > Would anybody be able to confirm this problem exists? > Many thanks, L. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.This email message may contain legally privileged and/or...{{dropped:2}}
On 16/06/18 13:09, Martin Morgan wrote:> mzR is a Bioconductor package so you might have more luck contacting > the maintainer on the Bioconductor support site > > ? https://support.bioconductor.org > > or on the 'bioc-devel' mailing list > > ? https://stat.ethz.ch/mailman/listinfo/bioc-devel > > or most directly by opening an issue on the maintainer's github > > ? https://github.com/sneumann/mzR/issues/ > > this is linked to from the package 'landing page' > > ? https://bioconductor.org/packages/mzR > > Martin Morgan > > On 06/15/2018 10:49 AM, lejeczek via R-help wrote: >> hi guys, just an admin here. >> >> I wonder if anybody see what I see, or similar? I'm on Centos 7.x and >> this occurs with R 3.4.x 3.5.x and probably earlier versions too. >> >> Every time I use something like -j>1 to pass to a compiler, eg.echo -ne >> >> $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n >> source(\"https://bioconductor.org/biocLite.R\")\\n >> biocLite(c(\"mzR\"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE, >> ask=FALSE)" | /usr/bin/R --vanilla >> >> mzR fails to compile: >> ... >> g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o >> ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o >> ./boost/libs/regex/src/regex_raw_buffer.o >> ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o >> ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o >> ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o >> ./boost/libs/regex/src/wide_posix_api.o >> ./boost/libs/regex/src/regex_traits_defaults.o >> ./boost/libs/regex/src/winstances.o >> ./boost/libs/regex/src/wc_regex_traits.o >> ./boost/libs/regex/src/c_regex_traits.o >> ./boost/libs/regex/src/cpp_regex_traits.o >> ./boost/libs/regex/src/static_mutex.o >> ./boost/libs/regex/src/w32_regex_traits.o >> ./boost/libs/iostreams/src/zlib.o >> ./boost/libs/iostreams/src/file_descriptor.o >> ./boost/libs/filesystem/src/operations.o >> ./boost/libs/filesystem/src/path.o >> ./boost/libs/filesystem/src/utf8_codecvt_facet.o >> ./boost/libs/chrono/src/chrono.o >> ./boost/libs/chrono/src/process_cpu_clocks.o >> ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o >> ./pwiz/data/identdata/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/mz5/Configuration_mz5.o >> ./pwiz/data/msdata/mz5/Connection_mz5.o >> ./pwiz/data/msdata/mz5/Datastructures_mz5.o >> ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o >> ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o >> ./pwiz/data/msdata/mz5/Translator_mz5.o >> ./pwiz/data/msdata/SpectrumList_MGF.o >> ./pwiz/data/msdata/DefaultReaderList.o >> ./pwiz/data/msdata/ChromatogramList_mzML.o >> ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 ./boost/libs/thread/src/pthread/once.o >> ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o >> -lpthread /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a >> /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a >> /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ >> -lnetcdf -L/usr/lib64/R/lib -lR >> g++: error: cramp.o: No such file or directory >> make: *** [mzR.so] Error 1 >> ERROR: compilation failed for package ?mzR? >> * removing ?/usr/lib64/R/library/mzR? >> >> If j is 1, then compilation succeeds. >> I have hundreds of packages and so far only "mzR" and "MSnbase" fail >> if I compile with -j>1. >> >> Would anybody be able to confirm this problem exists? >> Many thanks, L. >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > 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.sure sure, Could somebody just run compilation the way I described it and confirm it fails? Anybody on Centos/rhel? many thanks, L.