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

[lejeczek]

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.
>>
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sure sure,

Could somebody just run compilation the way I described it and confirm 
it fails? Anybody on Centos/rhel?

many thanks, L.