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@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@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....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-help@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.
