From peljasz at yahoo.co.uk  Wed Dec 21 18:00:36 2016
From: peljasz at yahoo.co.uk (lejeczek)
Date: Wed, 21 Dec 2016 17:00:36 +0000
Subject: [Rd] different compilers and mzR build fails
Message-ID: <967bf4dd-8f1a-0c16-a09f-1a4df61ac9a7@yahoo.co.uk>

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.



[Rd] different compilers and mzR build fails
lejeczek