From peljasz at yahoo.co.uk  Wed Dec 21 19:56:32 2016
From: peljasz at yahoo.co.uk (lejeczek)
Date: Wed, 21 Dec 2016 18:56:32 +0000
Subject: [Rd] different compilers and mzR build fails
In-Reply-To: <e28262f5-e03f-15b0-c4d2-dacb52898a51@roswellpark.org>
References: <967bf4dd-8f1a-0c16-a09f-1a4df61ac9a7@yahoo.co.uk>
	<e28262f5-e03f-15b0-c4d2-dacb52898a51@roswellpark.org>
Message-ID: <657a3fd6-465c-d2e8-5568-6941f596f078@yahoo.co.uk>


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
>
>
> This email message may contain legally privileged and/or 
> confidential information.  If you are not the intended 
> recipient(s), or the employee or agent responsible for the 
> delivery of this message to the intended recipient(s), you 
> are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  
> If you have received this message in error, please notify 
> the sender immediately by e-mail and delete this email 
> message from your computer. Thank you.



[Rd] different compilers and mzR build fails
lejeczek