{"action":"created","issue":{"url":"https://api.github.com/repos/sneumann/mzR/issues/72","repository_url":"https://api.github.com/repos/sneumann/mzR","labels_url":"https://api.github.com/repos/sneumann/mzR/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/sneumann/mzR/issues/72/comments","events_url":"https://api.github.com/repos/sneumann/mzR/issues/72/events","html_url":"https://github.com/sneumann/mzR/issues/72","id":197044083,"number":72,"title":"mzR fails to build with gcc 6.2.1","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-12-21T22:05:15Z","updated_at":"2016-12-22T14:04:56Z","closed_at":null,"body":"This [post](https://support.bioconductor.org/p/90546/) on the support site \r\n\r\n> I'm not sure if I should bother you team with this, apologies in case it's a bother.\r\n>\r\n> I'm trying gcc 6.2.1 (from devtoolset-6) with R, everything seems to work just fine, except for mzR.\r\n> Here is failed build:\r\n\r\n```\r\ng++ -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\r\ng++: error: cramp.o: No such file or directory\r\ng++: error: ramp_base64.o: No such file or directory\r\ng++: error: ramp.o: No such file or directory\r\ng++: error: RcppRamp.o: No such file or directory\r\ng++: error: RcppRampModule.o: No such file or directory\r\ng++: error: rnetCDF.o: No such file or directory\r\ng++: error: RcppPwiz.o: No such file or directory\r\ng++: error: RcppPwizModule.o: No such file or directory\r\ng++: error: RcppIdent.o: No such file or directory\r\ng++: error: RcppIdentModule.o: No such file or directory\r\n/usr/share/R/make/shlib.mk:6: recipe for target 'mzR.so' failed\r\nmake: *** [mzR.so] Error 1\r\n```\r\n> It did compile with 5.2.x (from devtoolset-4) and worked fine.\r\n> 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?\r\n\r\nAny idea?"},"comment":{"url":"https://api.github.com/repos/sneumann/mzR/issues/comments/268805904","html_url":"https://github.com/sneumann/mzR/issues/72#issuecomment-268805904","issue_url":"https://api.github.com/repos/sneumann/mzR/issues/72","id":268805904,"user":{"login":"lejeczek","id":1729865,"avatar_url":"https://avatars.githubusercontent.com/u/1729865?v=3","gravatar_id":"","url":"https://api.github.com/users/lejeczek","html_url":"https://github.com/lejeczek","followers_url":"https://api.github.com/users/lejeczek/followers","following_url":"https://api.github.com/users/lejeczek/following{/other_user}","gists_url":"https://api.github.com/users/lejeczek/gists{/gist_id}","starred_url":"https://api.github.com/users/lejeczek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lejeczek/subscriptions","organizations_url":"https://api.github.com/users/lejeczek/orgs","repos_url":"https://api.github.com/users/lejeczek/repos","events_url":"https://api.github.com/users/lejeczek/events{/privacy}","received_events_url":"https://api.github.com/users/lejeczek/received_events","type":"User","site_admin":false},"created_at":"2016-12-22T14:04:56Z","updated_at":"2016-12-22T14:04:56Z","body":"actually, mzR does not compile at all on eg. Centos 7.x in R-core-3.3.2-2.el7.x86_64.\r\nI've been now trying vanilla-plain distro's R and mzR fails the same exact way.\r\nI attached a log but I'm worried that might not be good enough.\r\n[mzR.compile-fails.txt](https://github.com/sneumann/mzR/files/668894/mzR.compile-fails.txt)\r\n\r\n"}}
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