Hello Ren?, you do not need to have root access to a machine to install your own versions of R and your favourite packages there. This is how to do it: 1. downloaded the tar.gz of the development version of R from ftp://ftp.stat.math.ethz.ch/Software/R/ 2. uncompress it to a directory you have write access to, say ~/local/R 3. change into the uncompressed directory, ~/local/R/R-devel 4. run "./configure" 5. run "make" Afterwards you can start R by executing ~/local/R/R-devel/bin/R; to simplify that either add the bin directory to your path or create an alias for R You do not need to run "make install" to work with R. For packages, 1. create a directory in which you want the packages installed, e.g. ~/local/rpacks 2. create an evironment variable R_LIBS that holds the path to that directory, e.g. "setenv R_LIBS=${HOME}/local/rpacks" with that directory and a C-shell (use export with a Bash shell) This environment variable tells R where to look first for installed packages and where to install packages when using "install.packages" or "biocLite". R_LIBS is safe to use, since it only extends the path to look for packages and does not replace the default R library path. I would recommend to add the alias for starting R and the R_LIBS definition to your shell startup file (~/.cshrc or ~/.bashrc). Regards, Joern Rene Dreos (JIC) wrote: > Herve, thanks a lot for your reply, but unfortunately R is installed on a machine for which I am not the root and the only user... so I can not easily upload R version without the approval of administrator and other users. > > Is it possible for me to build the Arabidopsis genome package by myself and use it with the older R and Biostrings versions? > > Cheers > Ren? > >

Hi Ren?, Rene Dreos (JIC) wrote: > Herve, thanks a lot for your reply, but unfortunately R is installed on a machine for which I am not the root and the only user... so I can not easily upload R version without the approval of administrator and other users. > > Is it possible for me to build the Arabidopsis genome package by myself and use it with the older R and Biostrings versions? Unfortunately this is not simple because of the numerous things that have changed in Biostrings/BSgenome since BioC 2.1 and the latest BSgenome packages in BioC 2.2 rely on these changes in order to work properly. Hopefully you manage to download and compile your own instance of R-2.7.0 as Joern suggested. This is very easy to do on Linux and, in case you are stuck, there is a lot of useful information and resources available around on this topic (like the R-help mailing list and the "R Installation and Administration" manual on CRAN). Cheers, H. > > Cheers > Ren? > > > -----Original Message----- > From: Herve Pages [mailto:hpages at fhcrc.org] > Sent: 14 April 2008 20:27 > To: Rene Dreos (JIC) > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Biostrings and A. thaliana genome sequence > > Hi Ren?, > > Rene Dreos (JIC) wrote: >> Hello list, >> >> >> >> I would like to use Biostrings to work with A. thaliana genome sequence. But, when I tried to extract the sequence from BSgenome.Athaliana.TAIR.01222004 library I've got the following errors. Does anyone know why this happen and how I can solve it? >> >> >> >>> library("Biostrings", lib.loc="/common/users/dreosr/unix/software/lib") >>> library("BSgenome", lib.loc="/common/users/dreosr/unix/software/lib") >>> library("BSgenome.Athaliana.TAIR.01222004", lib.loc="/common/users/dreosr/unix/software/lib") >>> Athaliana$chr1 >> Error in readChar(con, 5) : cannot open the connection >> >> In addition: Warning message: >> >> In readChar(con, 5) : >> >> cannot open compressed file '', probable reason 'No such file or directory' >> >>> Athaliana[[chr1]] >> Error in readChar(con, 5) : cannot open the connection >> >> In addition: Warning message: >> >> In readChar(con, 5) : >> >> cannot open compressed file '', probable reason 'No such file or directory' >> >> >> >>> sessionInfo() >> R version 2.6.2 (2008-02-08) >> >> x86_64-redhat-linux-gnu >> >> >> >> locale: >> >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en _GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_ GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UT F-8;LC_IDENTIFICATION=C >> >> >> >> attached base packages: >> >> [1] grid splines tools stats graphics grDevices utils >> >> [8] datasets methods base >> >> >> >> other attached packages: >> >> [1] BSgenome.Athaliana.TAIR.01222004_1.3.1 >> >> [2] BSgenome_1.6.2 >> >> [3] Biostrings_2.6.6 >> >> [4] WiggeNorm_1.0 >> >> [5] quantsmooth_1.4.0 >> >> [6] quantreg_4.17 >> >> [7] SparseM_0.75 >> >> [8] lodplot_1.1 >> >> [9] gcrma_2.10.0 >> >> [10] matchprobes_1.10.0 >> >> [11] affxparser_1.10.2 >> >> [12] affy_1.16.0 >> >> [13] preprocessCore_1.0.0 >> >> [14] affyio_1.6.1 >> >> [15] Biobase_1.16.3 >> >> > > You are using R 2.6.2 + BioC 2.1 (current release) but BSgenome.Athaliana.TAIR.01222004 1.3.1 > belongs to BioC 2.2 so unless you know exactly what you are doing, this is not a recommended > situation. > Anyway, because of some recent changes in Biostrings/BSgenome, BSgenome.Athaliana.TAIR.01222004 > 1.3.1 was broken even for R-2.7.0 + BioC 2.2 users. I've fixed it and the new version of the > package (1.3.3) will be available thru biocLite() in about 30 minutes. Note that you need > R-2.7.0 + the latest versions of Biostrings/BSgenome in order to use any of the latest versions > of the BSgenome.* packages (1.3.3, the 1.3.1 versions are broken and will be fixed ASAP). > > Cheers, > H.