different compilers and mzR build fails

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.

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