[R] problem in saving the history file '~/.Rhistory'
hi guys,
I'm on Centos 7.6 with R 3.6 and I see this:
>
Save workspace image? [y/n/c]: y
Warning message:
problem in saving the history file '~/.Rhistory'
from strace:
rt_sigaction(SIGWINCH, {SIG_DFL, [], SA_RESTORER, 0x7fb9dd34b5d0},
{0x7fb9dc383820, [], SA_RESTORER|SA_RESTART, 0x7fb9dd34b5d0}, 8) = 0
rt_sigprocmask(SIG_BLOCK, [INT], [], 8) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
ioctl(1, TCXONC, TCOON) = 0
open("~/.Rhistory", O_WRONLY|O_CREAT|O_TRUNC, 0600) = -1 ENOENT (No such
file or directory)
brk(NULL) = 0x43da000
brk(0x43fe000) = 0x43fe000
rt_sigaction(SIGINT, {SIG_IGN, [], SA_RESTORER, 0x7fb9dcfa2280},
{0x7fb9dfd99ffb, [INT], SA_RESTORER|SA_RESTART, 0x7fb9dd34b5d0}, 8) = 0
rt_sigaction(SIGQUIT, {SIG_IGN, [], SA_RESTORER, 0x7fb9dcfa2280},
{SIG_DFL, [], SA_RESTORER, 0x7fb9dd34b5d0}, 8) = 0
rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0
clone(child_stack=0, flags=CLONE_PARENT_SETTID|SIGCHLD,
parent_tidptr=0x7ffd7d87e100) = 1367359
wait4(1367359, [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 1367359
rt_sigaction(SIGINT, {0x7fb9dfd99ffb, [INT], SA_RESTORER|SA_RESTART,
0x7fb9dcfa2280}, NULL, 8) = 0
rt_sigaction(SIGQUIT, {SIG_DFL, [], SA_RESTORER, 0x7fb9dcfa2280}, NULL,
8) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=1367359,
si_uid=0, si_status=0, si_utime=0, si_stime=1} ---
write(2, "Warning message:\n", 17) = 17
write(2, "problem in saving the history fi"..., 50) = 50
exit_group(0) = ?
+++ exited with 0 +++
This only with user "root", and the some root can touch the ~/.Rhistory
just fine.
Even this works:
> system(command="touch ~/.Rhistory")
Would have any suggestions, ideas on how to fix it?
many thanks, L.
__
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Re: [R] mzR fails to install/compile (linuxes)
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.
[R] rgdal in 3.5 fails(?)
hi there installation of the package fails: ... g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I/tmp/RtmpPEjOIB/R.INSTALL952df53b77184/rgdal/inst/include -I/tmp/RtmpPEjOIB/R.INSTALL952df53b77184/rgdal/inst/include -I"/usr/lib64/R/library/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I/tmp/RtmpPEjOIB/R.INSTALL952df53b77184/rgdal/inst/include -I/tmp/RtmpPEjOIB/R.INSTALL952df53b77184/rgdal/inst/include -I"/usr/lib64/R/library/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o gdal-bindings.cpp: In function ‘SEXPREC* RGDAL_GDALwithGEOS()’: gdal-bindings.cpp:334:81: error: no matching function for call to ‘OGRGeometryFactory::createFromWkt(const char*, NULL, OGRGeometry**)’ OGRGeometryFactory::createFromWkt( (const char*) pszWKT, NULL, ); ^ gdal-bindings.cpp:334:81: note: candidate is: In file included from /usr/include/gdal/ogr_feature.h:34:0, from /usr/include/gdal/ogrsf_frmts.h:35, from gdal-bindings.cpp:7: /usr/include/gdal/ogr_geometry.h:663:19: note: static OGRErr OGRGeometryFactory::createFromWkt(char**, OGRSpatialReference*, OGRGeometry**) static OGRErr createFromWkt( char **, OGRSpatialReference *, ^ /usr/include/gdal/ogr_geometry.h:663:19: note: no known conversion for argument 1 from ‘const char*’ to ‘char**’ gdal-bindings.cpp:340:81: error: no matching function for call to ‘OGRGeometryFactory::createFromWkt(const char*, NULL, OGRGeometry**)’ OGRGeometryFactory::createFromWkt( (const char*) pszWKT, NULL, ); Would you know is this the package's problem in new 3.5 version? Many thanks, L. __ R-help@r-project.org 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.
[R] mzR fails to install/compile (linuxes)
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
[R] R re-base/compile problem
hi everyone. this will be a bit rpm packaging related, not sure if more than R itself but before going to rpm gang I hoped someone here knows: why this: byte-compiling package 'compiler' Warning in file(datafile, "wb") : cannot open file '/usr/lib64/R-MY/lib64/R/library/compiler/R/compiler.rdb': Permission denied Error in file(datafile, "wb") : cannot open the connection Calls: -> code2LazyLoadDB -> makeLazyLoadDB -> close -> file Execution halted happens when I rpmbuild R? I do a bit of mangling there, but nothing in the sources of R, just rpm spec files & paths. Why build process would call this file? (which is not there anyway) Weirder is that if rpm packages (of that my custom build) are already installed that problem occurs, build fails only then. Suffice to yum/rpm uninstall those R-MY* packages and rpm build process is successful. To me it's strangest thing, but an expert hopefully knows what is going on there. many thanks, L. __ R-help@r-project.org 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.
