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. 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