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? ?? <pengchy1981 at="" yahoo.com.cn=""> writes: > hi,all > > I run R & Bioconductor on SUSE LINUX Enterprise Server 9(x86_64) > The R is complied from the source file R-2.4.1.tar.gz, and the used packages are all installed from the source file with the command: > > >install.packages("/bwdata/bdb/pengchy/R/library/package.tar.gz", repos=NULL) > > What confused me is several packages can't be installed because the depend package can't be loaded. Take 'siggenes' package for example: > > > install.packages("/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.t ar.gz",repos=NULL) Please read some of the documentation. The way to install Bioconductor packages is to use biocLite. So try this from a fresh R session: source("http://bioconductor.org/biocLite.R") biocLite("multtest") + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Hi ? ??, ? ?? wrote: > hi,all > > I run R & Bioconductor on SUSE LINUX Enterprise Server 9(x86_64) > The R is complied from the source file R-2.4.1.tar.gz, and the used packages are all installed from the source file with the command: > > >install.packages("/bwdata/bdb/pengchy/R/library/package.tar.gz", repos=NULL) This is bad idea. I'm not surprised that you get a lot of dependency problems. The correct and recommended way to install Bioconductor packages is to use biocLite(): http://bioconductor.org/docs/install-howto.html Any given Bioconductor package can have dependencies that live in other repositories than the Bioconductor software repo itself (including CRAN) so, unless you've downloaded the content of all those repositories to your local disk too, you will end up with many many missing dependencies... Cheers, H. > > What confused me is several packages can't be installed because the depend package can't be loaded. Take 'siggenes' package for example: > > > install.packages("/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.t ar.gz",repos=NULL) > > * Installing *source* package 'siggenes' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: multtest > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > Loading required package: survival > Loading required package: splines > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so': > /bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory > Error: package 'multtest' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'siggenes' > ** Removing '/bwdata/bdb/pengchy/R-2.4.1/library/siggenes' > Warning message: > installation of package '/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.tar.gz' had non-zero exit status in: install.packages("/bwdata/bdb/pengchy/R/library/siggen es_1.8.0.tar.gz", > > when I load 'multtest' following is the returned message: > > >library(multtest) > Loading required package: survival > Loading required package: splines > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so': > /home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory > Error: package/namespace load failed for 'multtest' > > The same problem happen to some other packages, such as: 'vsn', 'akima',etc. > > Some one meet the same problem on Mac OX, and "created a symlink (from libs/multtest.so to libs/ppc/multtest.so)", but it doesn't work on SUSE. > > Anyone can help me will be appreciated! > > > Best wishes! > > Sincerely, pengcheng > > > --------------------------------- > ????????????????-3.5G??????20M?????? > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi, I happened to have the same problem a couple of days ago on my mac ox (probably you found that question too). I just provide my solution here: just simply re-install R. :) Also, I suggest you to ask this type of question in R-list instead of bioconductor. HTH, Weiwei On 4/15/07, ?? ???? <pengchy1981 at="" yahoo.com.cn=""> wrote: > hi,all > > I run R & Bioconductor on SUSE LINUX Enterprise Server 9(x86_64) > The R is complied from the source file R-2.4.1.tar.gz, and the used packages are all installed from the source file with the command: > > >install.packages("/bwdata/bdb/pengchy/R/library/package.tar.gz", repos=NULL) > > What confused me is several packages can't be installed because the depend package can't be loaded. Take 'siggenes' package for example: > > > install.packages("/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.t ar.gz",repos=NULL) > > * Installing *source* package 'siggenes' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: multtest > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > Loading required package: survival > Loading required package: splines > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so': > /bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory > Error: package 'multtest' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'siggenes' > ** Removing '/bwdata/bdb/pengchy/R-2.4.1/library/siggenes' > Warning message: > installation of package '/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.tar.gz' had non-zero exit status in: install.packages("/bwdata/bdb/pengchy/R/library/siggen es_1.8.0.tar.gz", > > when I load 'multtest' following is the returned message: > > >library(multtest) > Loading required package: survival > Loading required package: splines > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so': > /home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory > Error: package/namespace load failed for 'multtest' > > The same problem happen to some other packages, such as: 'vsn', 'akima',etc. > > Some one meet the same problem on Mac OX, and "created a symlink (from libs/multtest.so to libs/ppc/multtest.so)", but it doesn't work on SUSE. > > Anyone can help me will be appreciated! > > > Best wishes! > > Sincerely, pengcheng > > > --------------------------------- > ????????????????-3.5G??????20M?????? > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III