[Rd] different compilers and mzR build fails

Martin Morgan martin.morgan at roswellpark.org
Wed Dec 21 22:08:05 CET 2016

On 12/21/2016 01:56 PM, lejeczek wrote:
> I do this on a vanilla-clean R installation, simply:
>> biocLite("mzR")
> it pulls some deps in which compile fine, only mzR fails.
> ... meanwhile...
> I grabbed devtools and comiled github master - still fails.
> Should I attach build log? One should not send attachments to the list..
> I don't suppose?

My opinion is that the appropriate forum is the Bioconductor support 
site. I think you should EDIT your question on the Bioconductor support 
site to add the compiler output. If you feel like you can spot where 
things are going wrong, then edited to include those parts otherwise 
post the output in its entirety; the support site can mangle formatting, 
so I'd copy-and-paste the compiler output, and then select it and format 
it as 'code'.

If you feel that the current forum is more appropriate, then 
cut-and-paste the compiler output into an email message, avoding 


> On 21/12/16 17:06, Martin Morgan wrote:
>> mzR is a Bioconductor package, so better to ask on the Bioconductor
>> support forum
>>   https://support.bioconductor.org
>> Oh, I see you did, and then the advice is to avoid cross-posting!
>> The missing .o files would have been produced in an earlier
>> compilation step; they likely failed in some way, so you need to
>> provide the complete compilation output.
>> Did you do this on a version of the package that did not have any
>> previous build artifacts (e.g., via biocLite() or from a fresh svn
>> checkout)?
>> Martin
>> On 12/21/2016 12:00 PM, lejeczek via R-devel wrote:
>>> I'm not sure if I should bother you team with this, apologies in case
>>> it's a bother.
>>> I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything seems to
>>> work just fine, except for mzR.
>>> Here is failed build:
>>> g++ -m64 -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/system/src/error_code.o ./boost/regex/src/posix_api.o
>>> ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o
>>> ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o
>>> ./boost/regex/src/instances.o ./boost/regex/src/icu.o
>>> ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o
>>> ./boost/regex/src/wide_posix_api.o
>>> ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o
>>> ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o
>>> ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o
>>> ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o
>>> ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o
>>> ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o
>>> ./boost/filesystem/src/path.o
>>> ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o
>>> ./boost/chrono/src/process_cpu_clocks.o
>>> ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/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/SpectrumList_MGF.o
>>> ./pwiz/data/msdata/DefaultReaderList.o
>>> ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o
>>> ./pwiz/data/msdata/Serializer_mzXML.o
>>> ./pwiz/data/msdata/SpectrumList_mzML.o
>>> ./pwiz/data/msdata/SpectrumList_MSn.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
>>> rampR.o R_init_mzR.o -lpthread -lnetcdf -L/usr/lib64/R/lib -lR
>>> g++: error: cramp.o: No such file or directory
>>> g++: error: ramp_base64.o: No such file or directory
>>> g++: error: ramp.o: No such file or directory
>>> g++: error: RcppRamp.o: No such file or directory
>>> g++: error: RcppRampModule.o: No such file or directory
>>> g++: error: rnetCDF.o: No such file or directory
>>> g++: error: RcppPwiz.o: No such file or directory
>>> g++: error: RcppPwizModule.o: No such file or directory
>>> g++: error: RcppIdent.o: No such file or directory
>>> g++: error: RcppIdentModule.o: No such file or directory
>>> /usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' failed
>>> make: *** [mzR.so] Error 1
>>> It did compile with 5.2.x (from devtoolset-4) and worked fine.
>>> I'm hoping you guys could confirm it is purely compiler problem? Or
>>> point me(not a real programmer) a way to troubleshoot it properly?
>>> many thanks,
>>> L.
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
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