From martin.morgan at roswellpark.org  Wed Dec 21 18:06:59 2016
From: martin.morgan at roswellpark.org (Martin Morgan)
Date: Wed, 21 Dec 2016 12:06:59 -0500
Subject: [Rd] different compilers and mzR build fails
In-Reply-To: <967bf4dd-8f1a-0c16-a09f-1a4df61ac9a7@yahoo.co.uk>
References: <967bf4dd-8f1a-0c16-a09f-1a4df61ac9a7@yahoo.co.uk>
Message-ID: <e28262f5-e03f-15b0-c4d2-dacb52898a51@roswellpark.org>

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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[Rd] different compilers and mzR build fails
Martin Morgan