[R] mzR fails to install/compile (linuxes)

[Martin Morgan]

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.
> 
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