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lejeczek

2016-Dec-21 17:00 UTC

[Rd] different compilers and mzR build fails

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.

Martin Morgan

2016-Dec-21 17:06 UTC

head link

[Rd] 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.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

This email message may contain legally privileged and/or...{{dropped:2}}

lejeczek

2016-Dec-21 18:56 UTC

head link

[Rd] different compilers and mzR build fails

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?

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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