Marc Carlson <mcarlson at="" ...=""> writes: > > Hi Manikhandan, > > I am unable to reproduce this problem. Can you please give us your > sessionInfo() as described in the posting guide? > > http://www.bioconductor.org/docs/postingGuide.html > > I can tell you that none of the human chip packages will work without > the org.Hs.eg.db package installed so getting this installed is going to > be critical to your success. > > Marc Marc Carlson <mcarlson at="" ...=""> writes: > > Hi Manikhandan, > > I am unable to reproduce this problem. Can you please give us your > sessionInfo() as described in the posting guide? > > http://www.bioconductor.org/docs/postingGuide.html > > I can tell you that none of the human chip packages will work without > the org.Hs.eg.db package installed so getting this installed is going to > be critical to your success. > > Marc Dear Marc, Thanks very much. My sessionInfo: > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] e1071_1.5-24 class_7.3-2 samr_1.28 [4] impute_1.22.0 bridge_1.12.1 rama_1.22.1 [7] RankProd_2.20.0 AnnotationDbi_1.10.1 Biostrings_2.16.5 [10] IRanges_1.6.6 preprocessCore_1.10.0 affyio_1.16.0 [13] plgem_1.20.0 MASS_7.3-6 siggenes_1.22.0 [16] multtest_2.4.0 simpleaffy_2.24.0 gcrma_2.20.0 [19] genefilter_1.30.0 RColorBrewer_1.0-2 affydata_1.11.10 [22] affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] annotate_1.26.0 DBI_0.2-5 RSQLite_0.9-1 survival_2.35-8 [5] tools_2.11.1 xtable_1.5-6 > Thanks. Regards, Mani

Hi Manikhandan, I still cannot reproduce this problem. I have loaded all the latest versions of the packages that you have in your sessionInfo() and none of them causes any problems for me. But the error says that your annotation database is locked. And so I wonder if you might have other R sessions (or other things) open which are tapping into (and possibly writing to) this same library? So you might want to start over, and be sure to try and kill any rogue R processes that may be present, it might also be a good idea to start fresh by moving the .RData file from the directory you use to launch R. Another thing to try is to remove your previous annotation packages (in particular org.Hs.eg.db since that one is giving this error) with remove.packages(). That way you can get a fresh start when you try to use biocLite() to install these packages. Marc On 06/29/2010 09:57 AM, Manikhandan Mudaliar wrote: > Marc Carlson <mcarlson at="" ...=""> writes: > > >> Hi Manikhandan, >> >> I am unable to reproduce this problem. Can you please give us your >> sessionInfo() as described in the posting guide? >> >> http://www.bioconductor.org/docs/postingGuide.html >> >> I can tell you that none of the human chip packages will work without >> the org.Hs.eg.db package installed so getting this installed is going to >> be critical to your success. >> >> Marc >> > > Marc Carlson <mcarlson at="" ...=""> writes: > > >> Hi Manikhandan, >> >> I am unable to reproduce this problem. Can you please give us your >> sessionInfo() as described in the posting guide? >> >> http://www.bioconductor.org/docs/postingGuide.html >> >> I can tell you that none of the human chip packages will work without >> the org.Hs.eg.db package installed so getting this installed is going to >> be critical to your success. >> >> Marc >> > > > Dear Marc, > > Thanks very much. > > My sessionInfo: > > >> sessionInfo() >> > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] e1071_1.5-24 class_7.3-2 samr_1.28 > [4] impute_1.22.0 bridge_1.12.1 rama_1.22.1 > [7] RankProd_2.20.0 AnnotationDbi_1.10.1 Biostrings_2.16.5 > [10] IRanges_1.6.6 preprocessCore_1.10.0 affyio_1.16.0 > [13] plgem_1.20.0 MASS_7.3-6 siggenes_1.22.0 > [16] multtest_2.4.0 simpleaffy_2.24.0 gcrma_2.20.0 > [19] genefilter_1.30.0 RColorBrewer_1.0-2 affydata_1.11.10 > [22] affy_1.26.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.26.0 DBI_0.2-5 RSQLite_0.9-1 survival_2.35-8 > [5] tools_2.11.1 xtable_1.5-6 > >> > Thanks. > > Regards, > Mani > > _______________________________________________ > 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 > >