Question: Rsamtools installation error
0
gravatar for Wolfgang Raffelsberger
7.7 years ago by
Wolfgang Raffelsberger60 wrote:
Hi list, unfortunately I have one more time trouble installing Rsamtools on a Fedore 4.5.1-4 system (with R-2.14.1). The error message points towards Rsamtools.so (but this time I don't see any hints to elements parts of our Fedora system that might be updated). By the way, using command-line R CMD INSTALL Rsamtools_1.6.3.tar.gz gave the same error All other packages from biocLite() - expect ShortRead which depends on Rsamtools install properly. Any hints ? Thank's in advance, Wolfgang Here the code run : > source("http://www.bioconductor.org/biocLite.R") > biocLite("Rsamtools") ... (lots of messages from compiling) ... mkdir -p "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtoo ls/bcftools" mkdir -p "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabix" cp samtools/*.h "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtoo ls/" cp samtools/bcftools/*h "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtoo ls/bcftools/" cp tabix/*h "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabix/ " mkdir -p "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib" cp libbam.a libbcf.a libtabix.a "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib" gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o vcffile.o zip_compression.o -fopenmp /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbam.a /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbcf.a /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libtabix .a -lz -L/biolo/R_surf/R-2.14.1/lib64/R/lib -lR installing to /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... 'Rsamtools-Overview.Rnw' 'Rsamtools-UsingCLibraries.Rnw' ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamtools .so': /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamtool s.so: undefined symbol: packInt16 Error: loading failed Execution halted ERROR: loading failed * removing '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools' The downloaded packages are in '/tmp/RtmpsehjVG/downloaded_packages' Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'Rsamtools' had non-zero exit status > for completness : > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.1 > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3201 wolfgang.raffelsberger (at) igbmc.fr [[alternative HTML version deleted]]
shortread rsamtools • 915 views
ADD COMMENTlink modified 7.7 years ago by Martin Morgan ♦♦ 23k • written 7.7 years ago by Wolfgang Raffelsberger60
Answer: Rsamtools installation error
0
gravatar for Martin Morgan
7.7 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
On 02/07/2012 03:57 AM, Wolfgang Raffelsberger wrote: > Hi list, > unfortunately I have one more time trouble installing Rsamtools on a Fedore > 4.5.1-4 system (with R-2.14.1). > The error message points towards Rsamtools.so (but this time I don't see > any hints to elements parts of our Fedora system that might be updated). > > By the way, using command-line R CMD INSTALL Rsamtools_1.6.3.tar.gz gave > the same error > All other packages from biocLite() - expect ShortRead which depends on > Rsamtools install properly. > > Any hints ? > > Thank's in advance, > Wolfgang > > > Here the code run : > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("Rsamtools") > ... (lots of messages from compiling) ... > mkdir -p > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samt ools/bcftools" > mkdir -p > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabix" > cp samtools/*.h > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samt ools/" > cp samtools/bcftools/*h > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samt ools/bcftools/" > cp tabix/*h > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabi x/" > mkdir -p "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib" > cp libbam.a libbcf.a libtabix.a > "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib" > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so > Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o > bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o > tabixfile.o utilities.o vcffile.o zip_compression.o -fopenmp > /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbam.a > /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbcf.a > /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libtab ix.a > -lz -L/biolo/R_surf/R-2.14.1/lib64/R/lib -lR > installing to /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > *** tangling vignette sources ... > 'Rsamtools-Overview.Rnw' > 'Rsamtools-UsingCLibraries.Rnw' > ** testing if installed package can be loaded > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamtoo ls.so': > /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamt ools.so: > undefined symbol: packInt16 Hi Wolfgang -- I think a work-around is to edit RHOME/etc/Makeconf or ~/.R/Makevars so that CFLAGS includes -Dinline="" The problem is that samtools does not declare an inline function with the keyword 'static'; a user has asked about this on the samtools mailing list without effect, so I'll change this in the devel version of Rsamtools, version 1.7.30. Martin > Error: loading failed > Execution halted > ERROR: loading failed > * removing '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools' > > The downloaded packages are in > '/tmp/RtmpsehjVG/downloaded_packages' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'Rsamtools' had non-zero exit status >> > > for completness : >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] tools_2.14.1 >> > > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . > Wolfgang Raffelsberger, PhD > IGBMC, > 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France > Tel (+33) 388 65 3300 Fax (+33) 388 65 3201 > wolfgang.raffelsberger (at) igbmc.fr > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 7.7 years ago by Martin Morgan ♦♦ 23k
Hi Martin, thank you VERY much ! Your fast answer allowed me properly installing Rsamtools (and many users on our system will soon be quite happy). BioC help is really great !!! CFLAGS in RHOME/etc/Makeconf alone did not do the job, but after also changing FCFLAGS and FFLAGS (possibly both necessary) installation from command line worked nicely. Many thanks, Wolfgang 2012/2/7 Martin Morgan <mtmorgan@fhcrc.org> > On 02/07/2012 03:57 AM, Wolfgang Raffelsberger wrote: > >> Hi list, >> unfortunately I have one more time trouble installing Rsamtools on a >> Fedore >> 4.5.1-4 system (with R-2.14.1). >> The error message points towards Rsamtools.so (but this time I don't see >> any hints to elements parts of our Fedora system that might be updated). >> >> By the way, using command-line R CMD INSTALL Rsamtools_1.6.3.tar.gz gave >> the same error >> All other packages from biocLite() - expect ShortRead which depends on >> Rsamtools install properly. >> >> Any hints ? >> >> Thank's in advance, >> Wolfgang >> >> >> Here the code run : >> >> source("http://www.**bioconductor.org/biocLite.R<http: www.biocon="" ductor.org="" bioclite.r=""> >>> ") >>> biocLite("Rsamtools") >>> >> ... (lots of messages from compiling) ... >> mkdir -p >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> include/samtools/bcftools" >> mkdir -p >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> include/tabix" >> cp samtools/*.h >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> include/samtools/" >> cp samtools/bcftools/*h >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> include/samtools/bcftools/" >> cp tabix/*h >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> include/tabix/" >> mkdir -p "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> usrlib" >> cp libbam.a libbcf.a libtabix.a >> "/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/**usrlib" >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so >> Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o >> bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o >> tabixfile.o utilities.o vcffile.o zip_compression.o -fopenmp >> /linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> usrlib/libbam.a >> /linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> usrlib/libbcf.a >> /linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> usrlib/libtabix.a >> -lz -L/biolo/R_surf/R-2.14.1/**lib64/R/lib -lR >> installing to /linux/biolo/R_surf/R-2.14.1/** >> lib64/R/library/Rsamtools/libs >> ** R >> ** inst >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices ... >> *** tangling vignette sources ... >> 'Rsamtools-Overview.Rnw' >> 'Rsamtools-UsingCLibraries.**Rnw' >> ** testing if installed package can be loaded >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> libs/Rsamtools.so': >> /linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools/** >> libs/Rsamtools.so: >> undefined symbol: packInt16 >> > > Hi Wolfgang -- I think a work-around is to edit RHOME/etc/Makeconf or > ~/.R/Makevars so that CFLAGS includes > > -Dinline="" > > The problem is that samtools does not declare an inline function with the > keyword 'static'; a user has asked about this on the samtools mailing list > without effect, so I'll change this in the devel version of Rsamtools, > version 1.7.30. > > Martin > > Error: loading failed >> Execution halted >> ERROR: loading failed >> * removing '/linux/biolo/R_surf/R-2.14.1/**lib64/R/library/Rsamtools' >> >> The downloaded packages are in >> '/tmp/RtmpsehjVG/downloaded_**packages' >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'Rsamtools' had non-zero exit status >> >>> >>> >> for completness : >> >>> sessionInfo() >>> >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.2.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.14.1 >> >>> >>> >> >> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . >> Wolfgang Raffelsberger, PhD >> IGBMC, >> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France >> Tel (+33) 388 65 3300 Fax (+33) 388 65 3201 >> wolfgang.raffelsberger (at) igbmc.fr >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]
ADD REPLYlink written 7.7 years ago by Wolfgang Raffelsberger60
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