mzR fails to install/compile (linuxes)

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mzR fails to install/compile (linuxes)

R help mailing list-2
hi guys, just an admin here.

I wonder if anybody see what I see, or similar? I'm on Centos 7.x and
this occurs with R 3.4.x 3.5.x and probably earlier versions too.

Every time I use something like -j>1 to pass to a compiler, eg.echo -ne

$ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n
source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"),
suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" |
/usr/bin/R --vanilla

mzR fails to compile:
...
g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o
./boost/libs/regex/src/fileiter.o
./boost/libs/regex/src/regex_raw_buffer.o
./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o
./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o
./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o
./boost/libs/regex/src/wide_posix_api.o
./boost/libs/regex/src/regex_traits_defaults.o
./boost/libs/regex/src/winstances.o
./boost/libs/regex/src/wc_regex_traits.o
./boost/libs/regex/src/c_regex_traits.o
./boost/libs/regex/src/cpp_regex_traits.o
./boost/libs/regex/src/static_mutex.o
./boost/libs/regex/src/w32_regex_traits.o
./boost/libs/iostreams/src/zlib.o
./boost/libs/iostreams/src/file_descriptor.o
./boost/libs/filesystem/src/operations.o
./boost/libs/filesystem/src/path.o
./boost/libs/filesystem/src/utf8_codecvt_facet.o
./boost/libs/chrono/src/chrono.o
./boost/libs/chrono/src/process_cpu_clocks.o
./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o
./pwiz/data/identdata/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/mz5/Configuration_mz5.o
./pwiz/data/msdata/mz5/Connection_mz5.o
./pwiz/data/msdata/mz5/Datastructures_mz5.o
./pwiz/data/msdata/mz5/ReferenceRead_mz5.o
./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
./pwiz/data/msdata/mz5/Translator_mz5.o
./pwiz/data/msdata/SpectrumList_MGF.o
./pwiz/data/msdata/DefaultReaderList.o
./pwiz/data/msdata/ChromatogramList_mzML.o
./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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
./boost/libs/thread/src/pthread/once.o
./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread
/usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a
/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a
/usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/
-lnetcdf -L/usr/lib64/R/lib -lR
g++: error: cramp.o: No such file or directory
make: *** [mzR.so] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/usr/lib64/R/library/mzR’

If j is 1, then compilation succeeds.
I have hundreds of packages and so far only "mzR" and "MSnbase" fail if
I compile with -j>1.

Would anybody be able to confirm this problem exists?
Many thanks, L.

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Re: mzR fails to install/compile (linuxes)

Peter Dalgaard-2
This is almost certainly a Makefile error. Something (A) is relying on something (B) without stating the dependency explicitly in the Makefile. You can get away with that (sometimes) in a non-parallel make, because the sequence of compilations is such that B gets built before A. However, with a parallel make, one thread may try to build A before B gets built by another thread.

The fix is to add the dependency in the Makefile (plus any other issues of the same kind). In this case, AFAICT, you need

mzR.so: cramp.o

in addition to what might be there already and any other stuff that is also missing. If there is already something like

mzR.so: $(OBJECTS)

chances are that there is a deficient macro definition earlier on, so that cramp.o is not contained in OBJECTS.

-pd

> On 15 Jun 2018, at 16:49 , lejeczek via R-help <[hidden email]> wrote:
>
> hi guys, just an admin here.
>
> I wonder if anybody see what I see, or similar? I'm on Centos 7.x and this occurs with R 3.4.x 3.5.x and probably earlier versions too.
>
> Every time I use something like -j>1 to pass to a compiler, eg.echo -ne
>
> $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" | /usr/bin/R --vanilla
>
> mzR fails to compile:
> ...
> g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/ -lnetcdf -L/usr/lib64/R/lib -lR
> g++: error: cramp.o: No such file or directory
> make: *** [mzR.so] Error 1
> ERROR: compilation failed for package ‘mzR’
> * removing ‘/usr/lib64/R/library/mzR’
>
> If j is 1, then compilation succeeds.
> I have hundreds of packages and so far only "mzR" and "MSnbase" fail if I compile with -j>1.
>
> Would anybody be able to confirm this problem exists?
> Many thanks, L.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: mzR fails to install/compile (linuxes)

Martin Morgan-3
In reply to this post by R help mailing list-2
mzR is a Bioconductor package so you might have more luck contacting the
maintainer on the Bioconductor support site

   https://support.bioconductor.org

or on the 'bioc-devel' mailing list

   https://stat.ethz.ch/mailman/listinfo/bioc-devel

or most directly by opening an issue on the maintainer's github

   https://github.com/sneumann/mzR/issues/

this is linked to from the package 'landing page'

   https://bioconductor.org/packages/mzR

Martin Morgan

On 06/15/2018 10:49 AM, lejeczek via R-help wrote:

> hi guys, just an admin here.
>
> I wonder if anybody see what I see, or similar? I'm on Centos 7.x and
> this occurs with R 3.4.x 3.5.x and probably earlier versions too.
>
> Every time I use something like -j>1 to pass to a compiler, eg.echo -ne
>
> $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n
> source(\"https://bioconductor.org/biocLite.R\")\\n biocLite(c(\"mzR\"),
> suppressUpdates=FALSE, suppressAutoUpdate=FALSE, ask=FALSE)" |
> /usr/bin/R --vanilla
>
> mzR fails to compile:
> ...
> g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o
> ./boost/libs/regex/src/fileiter.o
> ./boost/libs/regex/src/regex_raw_buffer.o
> ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o
> ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o
> ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o
> ./boost/libs/regex/src/wide_posix_api.o
> ./boost/libs/regex/src/regex_traits_defaults.o
> ./boost/libs/regex/src/winstances.o
> ./boost/libs/regex/src/wc_regex_traits.o
> ./boost/libs/regex/src/c_regex_traits.o
> ./boost/libs/regex/src/cpp_regex_traits.o
> ./boost/libs/regex/src/static_mutex.o
> ./boost/libs/regex/src/w32_regex_traits.o
> ./boost/libs/iostreams/src/zlib.o
> ./boost/libs/iostreams/src/file_descriptor.o
> ./boost/libs/filesystem/src/operations.o
> ./boost/libs/filesystem/src/path.o
> ./boost/libs/filesystem/src/utf8_codecvt_facet.o
> ./boost/libs/chrono/src/chrono.o
> ./boost/libs/chrono/src/process_cpu_clocks.o
> ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o
> ./pwiz/data/identdata/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/mz5/Configuration_mz5.o
> ./pwiz/data/msdata/mz5/Connection_mz5.o
> ./pwiz/data/msdata/mz5/Datastructures_mz5.o
> ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o
> ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
> ./pwiz/data/msdata/mz5/Translator_mz5.o
> ./pwiz/data/msdata/SpectrumList_MGF.o
> ./pwiz/data/msdata/DefaultReaderList.o
> ./pwiz/data/msdata/ChromatogramList_mzML.o
> ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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
> ./boost/libs/thread/src/pthread/once.o
> ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -lpthread
> /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a
> /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a
> /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/
> -lnetcdf -L/usr/lib64/R/lib -lR
> g++: error: cramp.o: No such file or directory
> make: *** [mzR.so] Error 1
> ERROR: compilation failed for package ‘mzR’
> * removing ‘/usr/lib64/R/library/mzR’
>
> If j is 1, then compilation succeeds.
> I have hundreds of packages and so far only "mzR" and "MSnbase" fail if
> I compile with -j>1.
>
> Would anybody be able to confirm this problem exists?
> Many thanks, L.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: mzR fails to install/compile (linuxes)

R help mailing list-2
On 16/06/18 13:09, Martin Morgan wrote:

> mzR is a Bioconductor package so you might have more luck contacting
> the maintainer on the Bioconductor support site
>
>   https://support.bioconductor.org
>
> or on the 'bioc-devel' mailing list
>
>   https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> or most directly by opening an issue on the maintainer's github
>
>   https://github.com/sneumann/mzR/issues/
>
> this is linked to from the package 'landing page'
>
>   https://bioconductor.org/packages/mzR
>
> Martin Morgan
>
> On 06/15/2018 10:49 AM, lejeczek via R-help wrote:
>> hi guys, just an admin here.
>>
>> I wonder if anybody see what I see, or similar? I'm on Centos 7.x and
>> this occurs with R 3.4.x 3.5.x and probably earlier versions too.
>>
>> Every time I use something like -j>1 to pass to a compiler, eg.echo -ne
>>
>> $ "Sys.setenv(MAKEFLAGS = \"-j2\")\\n
>> source(\"https://bioconductor.org/biocLite.R\")\\n
>> biocLite(c(\"mzR\"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE,
>> ask=FALSE)" | /usr/bin/R --vanilla
>>
>> mzR fails to compile:
>> ...
>> g++ -m64 -std=gnu++11 -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/libs/system/src/error_code.o
>> ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o
>> ./boost/libs/regex/src/regex_raw_buffer.o
>> ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o
>> ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o
>> ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o
>> ./boost/libs/regex/src/wide_posix_api.o
>> ./boost/libs/regex/src/regex_traits_defaults.o
>> ./boost/libs/regex/src/winstances.o
>> ./boost/libs/regex/src/wc_regex_traits.o
>> ./boost/libs/regex/src/c_regex_traits.o
>> ./boost/libs/regex/src/cpp_regex_traits.o
>> ./boost/libs/regex/src/static_mutex.o
>> ./boost/libs/regex/src/w32_regex_traits.o
>> ./boost/libs/iostreams/src/zlib.o
>> ./boost/libs/iostreams/src/file_descriptor.o
>> ./boost/libs/filesystem/src/operations.o
>> ./boost/libs/filesystem/src/path.o
>> ./boost/libs/filesystem/src/utf8_codecvt_facet.o
>> ./boost/libs/chrono/src/chrono.o
>> ./boost/libs/chrono/src/process_cpu_clocks.o
>> ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o
>> ./pwiz/data/identdata/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/mz5/Configuration_mz5.o
>> ./pwiz/data/msdata/mz5/Connection_mz5.o
>> ./pwiz/data/msdata/mz5/Datastructures_mz5.o
>> ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o
>> ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
>> ./pwiz/data/msdata/mz5/Translator_mz5.o
>> ./pwiz/data/msdata/SpectrumList_MGF.o
>> ./pwiz/data/msdata/DefaultReaderList.o
>> ./pwiz/data/msdata/ChromatogramList_mzML.o
>> ./pwiz/data/msdata/ChromatogramList_mz5.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_mz5.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/SpectrumList_mz5.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 ./boost/libs/thread/src/pthread/once.o
>> ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o
>> -lpthread /usr/lib64/R/library/Rhdf5lib/lib/libhdf5_cpp.a
>> /usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a
>> /usr/lib64/R/library/Rhdf5lib/lib/libsz.a -lz -L/opt/lib/hdf5-18/lib/
>> -lnetcdf -L/usr/lib64/R/lib -lR
>> g++: error: cramp.o: No such file or directory
>> make: *** [mzR.so] Error 1
>> ERROR: compilation failed for package ‘mzR’
>> * removing ‘/usr/lib64/R/library/mzR’
>>
>> If j is 1, then compilation succeeds.
>> I have hundreds of packages and so far only "mzR" and "MSnbase" fail
>> if I compile with -j>1.
>>
>> Would anybody be able to confirm this problem exists?
>> Many thanks, L.
>>
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>> and provide commented, minimal, self-contained, reproducible code.
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sure sure,

Could somebody just run compilation the way I described it and confirm
it fails? Anybody on Centos/rhel?

many thanks, L.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.