Hello everybody, tried to install bioconductor from three different machines (all 64 bits) and different OS (Linux different kernels, Windows XP) but always got a message like this one: > > source("http://bioconductor.org/biocLite.R") > > biocLite() > Running biocinstall version 2.2.9 with R version 2.7.0 > Your version of R requires version 2.2 of BioConductor. > Will install the following packages: > [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" > [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" > [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" > [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : > argument 'lib' is missing: using '/home/xxxxxxxx' > Error: subscript out of bounds > In addition: There were 15 warnings (use warnings() to see them) > Think that is something related to the place because at home (linux ubuntu 8.04, 32 bits) I was able to install it without problem Any idea? Thanks Daniel Silberschmidt

Hi Daniel -- Daniel Silberschmidt wrote: > Hello everybody, > tried to install bioconductor from three different machines (all 64 > bits) and different OS (Linux different kernels, Windows XP) but always > got a message like this one: > > > >>> source("http://bioconductor.org/biocLite.R") >>> biocLite() >> Running biocinstall version 2.2.9 with R version 2.7.0 >> Your version of R requires version 2.2 of BioConductor. >> Will install the following packages: >> [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" >> [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" >> [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" >> [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" >> Please wait... >> >> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : >> argument 'lib' is missing: using '/home/xxxxxxxx' >> Error: subscript out of bounds >> In addition: There were 15 warnings (use warnings() to see them) >> > > Think that is something related to the place because at home (linux ubuntu 8.04, 32 bits) I was able to install it without problem Hard to know for sure. After the error, what does traceback() say? Also, is /home/xxxxxxx really the directory where you are installing libraries? Perhaps a helpful system administrator has written a Rprofile file for the site that sets 'your' home directory to this. What does .libPaths() say? The packages will be installed in the first directory returned by .libPaths(), and you must have write permissions. If this is the issue, you'll want to configure R to know about a more sensible directory; see ?Startup and ?.libPaths for more. Hope that helps... Martin > Any idea? > > Thanks > > Daniel Silberschmidt > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Daniel and I identified the problem: a filter on Daniel's end did not allow downloading of the PACKAGES.gz file needed to retrieve packages. For the record, the filter complained that the MIME class application/x-gzip was not permitted. It only reported this for the http://cran.fhcrc.org address. Also for the record, we found this out by typing > warnings() after biocLite() failed. This suggested that read.dcf (called in available.packages) tried to parse a file that contained the html message generated by the filter. We then used debug(available.packages); biocLite() and stepped through the function until we found the repository that was causing the problem. Martin Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > Hi Daniel -- > > Daniel Silberschmidt wrote: >> Hello everybody, >> tried to install bioconductor from three different machines (all 64 >> bits) and different OS (Linux different kernels, Windows XP) but always >> got a message like this one: >> >>>> source("http://bioconductor.org/biocLite.R") >>>> biocLite() >>> Running biocinstall version 2.2.9 with R version 2.7.0 Your version >>> of R requires version 2.2 of BioConductor. >>> Will install the following packages: >>> [1] "affy" "affydata" "affyPLM" "annaffy" >>> "annotate" [6] "Biobase" "Biostrings" "DynDoc" >>> "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" >>> "limma" "marray" "matchprobes" [16] "multtest" >>> "ROC" "vsn" "xtable" "affyQCReport" >>> Please wait... >>> >>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : >>> argument 'lib' is missing: using '/home/xxxxxxxx' >>> Error: subscript out of bounds >>> In addition: There were 15 warnings (use warnings() to see them) >>> >> Think that is something related to the place because at home >> (linux ubuntu 8.04, 32 bits) I was able to install it without >> problem > > Hard to know for sure. After the error, what does traceback() say? > > Also, is /home/xxxxxxx really the directory where you are installing > libraries? Perhaps a helpful system administrator has written a > Rprofile file for the site that sets 'your' home directory to > this. What does .libPaths() say? The packages will be installed in the > first directory returned by .libPaths(), and you must have write > permissions. If this is the issue, you'll want to configure R to know > about a more sensible directory; see ?Startup and ?.libPaths for more. > > Hope that helps... > > Martin > > >> Any idea? Thanks >> Daniel Silberschmidt >> _______________________________________________ >> 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 > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793