I have never managed to use "getBioC" to install bioconductor from a unix machine. I have appended my latest effort below: 1. Can you tell me what stupid thing I am doing wrong? 2. Why does getBioC ignore my attempt to specify the destination directory, notice it tries to write to /usr/local/lib which I don't have write priveleges to. I certainly do have write priveleges to the directory I've specified. 3. Any thoughts why it takes getBioC 3-4 minutes to give me this error message? I can download reposTools using cvs from this machine in just a few seconds, so internet speed doesn't seem to be the problem. Thanks Gordon > source("http://www.bioconductor.org/getBioC.R") > system("pwd") /home/users/lab0605/smyth/gordon > getBioC(libName="all",relLevel="devel",destdir="/home/users/lab0605/sm yth/gordon/Rlibs") Running getBioC version 1.2.34.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Installing reposTools ..." ERROR: cannot write to or create directory '/usr/local/lib/R/library' Loading required package: Biobase Welcome to Bioconductor To view some introductory material -- look at our vignettes Simply type: openVignette() to see the available vignettes To read a vignette see the openVignette help page for details Creating a new generic function for "summary" in package Biobase Synching your local package management information ... Error in file(file, "wb") : unable to open connection In addition: Warning message: cannot open file `/usr/local/lib/R/library/liblisting.Rda' > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.0 year 2003 month 04 day 16 language R

I'm not sure if the error is related to bugs regarding connections mentioned as fixed, according to the release notes for 1.7.1? best, -tony Gordon Smyth <smyth@wehi.edu.au> writes: > I have never managed to use "getBioC" to install bioconductor from a > unix machine. I have appended my latest effort below: > > 1. Can you tell me what stupid thing I am doing wrong? > 2. Why does getBioC ignore my attempt to specify the destination > directory, notice it tries to write to /usr/local/lib which I don't > have write priveleges to. I certainly do have write priveleges to the > directory I've specified. > 3. Any thoughts why it takes getBioC 3-4 minutes to give me this error > message? I can download reposTools using cvs from this machine in just > a few seconds, so internet speed doesn't seem to be the problem. > > Thanks > Gordon > > > source("http://www.bioconductor.org/getBioC.R") > > system("pwd") > /home/users/lab0605/smyth/gordon > > getBioC(libName="all",relLevel="devel",destdir="/home/users/lab06 05/smyth/gordon/Rlibs") > Running getBioC version 1.2.34.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > [1] "Installing reposTools ..." > ERROR: cannot write to or create directory '/usr/local/lib/R/library' > Loading required package: Biobase > Welcome to Bioconductor > To view some introductory material -- look at our vignettes > Simply type: openVignette() > to see the available vignettes > To read a vignette see the openVignette help page for details > Creating a new generic function for "summary" in package > Biobase > > Synching your local package management information ... > Error in file(file, "wb") : unable to open connection > In addition: Warning message: > cannot open file `/usr/local/lib/R/library/liblisting.Rda' > > version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 1 > minor 7.0 > year 2003 > month 04 > day 16 > language R > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- A.J. Rossini / rossini@u.washington.edu / rossini@scharp.org http://software.biostat.washington.edu/ UNTIL IT MOVES IN JULY. Biomedical and Health Informatics, University of Washington Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center. FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}