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.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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