Hello everyone I am trying to install the human genome but I am facing an unusual problem here is the error message > biocLite("BSgenome.Hsapiens.UCSC.hg18") Running biocinstall version 2.2.11 with R version 2.7.2 Your version of R requires version 2.2 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/fs/sh-code/Software/RLIBS/' trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src/c ontrib/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz' Content type 'application/x-gzip' length 874579720 bytes (834.1 Mb) opened URL ======================================== downloaded 834.1 Mb tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes tar: Skipping to next header tar: Archive contains obsolescent base-64 headers tar: Error exit delayed from previous errors ERROR: cannot extract package from '/tmp/RtmprYAQfG/downloaded_package s/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz' The downloaded packages are in /tmp/RtmprYAQfG/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'BSgenome.Hsapiens.UCSC.hg18' had non-zero exit status Is this "tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes" related to a quota or an available space ? this is the only reason I can imagine. Thanks for your help Rad Radhouane Aniba Bioinformatics Postdoctoral Research Scientist Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology (CBCB) University of Maryland, College Park MD 20742

did you check how much space is left in /tmp and /fs on your computer? it is trying to extract the per-chromosome data files and running out of space, or so it seems. On Mon, Feb 13, 2012 at 12:00 PM, Mohamed Radhouane Aniba <aradwen@gmail.com> wrote: > Hello everyone > > I am trying to install the human genome but I am facing an unusual problem > here is the error message > > > biocLite("BSgenome.Hsapiens.UCSC.hg18") > Running biocinstall version 2.2.11 with R version 2.7.2 > Your version of R requires version 2.2 of BioConductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using '/fs/sh-code/Software/RLIBS/' > trying URL ' > http://bioconductor.org/packages/2.2/data/annotation/src/contrib/BSg enome.Hsapiens.UCSC.hg18_1.3.7.tar.gz > ' > Content type 'application/x-gzip' length 874579720 bytes (834.1 Mb) > opened URL > ======================================== > downloaded 834.1 Mb > > tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 > of 10240 bytes > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > tar: Error exit delayed from previous errors > ERROR: cannot extract package from > '/tmp/RtmprYAQfG/downloaded_packages/BSgenome.Hsapiens.UCSC.hg18_1.3 .7.tar.gz' > > The downloaded packages are in > /tmp/RtmprYAQfG/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'BSgenome.Hsapiens.UCSC.hg18' had non-zero exit > status > > > Is this "tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote > only 6656 of 10240 bytes" related to a quota or an available space ? > this is the only reason I can imagine. > > Thanks for your help > > Rad > > > > > > > Radhouane Aniba > Bioinformatics Postdoctoral Research Scientist > Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology (CBCB) > University of Maryland, College Park > MD 20742 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

Hi Mohamed, Any reason why you are using a 4 year old version of R / Bioconductor? I can't tell what's causing the tar extraction problem you are facing, and maybe you'll still have this problem with the latest version of R / Bioconductor (R 2.14, BioC 2.9), but, at least, by updating your installation, you'll be running the same version as everybody else on this list, which is also the only version we support. Cheers, H. On 02/13/2012 12:00 PM, Mohamed Radhouane Aniba wrote: > Hello everyone > > I am trying to install the human genome but I am facing an unusual problem > here is the error message > >> biocLite("BSgenome.Hsapiens.UCSC.hg18") > Running biocinstall version 2.2.11 with R version 2.7.2 > Your version of R requires version 2.2 of BioConductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : > argument 'lib' is missing: using '/fs/sh-code/Software/RLIBS/' > trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src /contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz' > Content type 'application/x-gzip' length 874579720 bytes (834.1 Mb) > opened URL > ======================================== > downloaded 834.1 Mb > > tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > tar: Error exit delayed from previous errors > ERROR: cannot extract package from '/tmp/RtmprYAQfG/downloaded_packa ges/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz' > > The downloaded packages are in > /tmp/RtmprYAQfG/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : > installation of package 'BSgenome.Hsapiens.UCSC.hg18' had non- zero exit status > > > Is this "tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes" related to a quota or an available space ? > this is the only reason I can imagine. > > Thanks for your help > > Rad > > > > > > > Radhouane Aniba > Bioinformatics Postdoctoral Research Scientist > Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology (CBCB) > University of Maryland, College Park > MD 20742 > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319