Hello everything, I have a question regarding the getTable function in the rtracklayer package. The code below used to work in previous R version, but it doesn't for the current release. I can't figure out what the problem is. Can anyone give some hint? Thanks for your help! Best, Arthur Xuejun Li City of Hope Comprehensive Cancer Center Department of Information Science 1500 East Duarte Road Duarte, CA 91010 - 3000 Ph: (626) 256-4673 ext. 65121 Fax: (626) 471-7106 > session <- browserSession() > genome(session) <- "mm9" > foo <- trackNames(session)[trackNames(session) =="rmsk"] > bar<- ucscTableQuery(session, foo) > bar1 <- getTable(bar) Error in if (st[["status"]] == 100) { : missing value where TRUE/FALSE needed > > > sessionInfo() R version 2.11.0 (2010-04-22) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.8.1 RCurl_1.4-1 bitops_1.0-4.1 [4] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 [7] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 loaded via a namespace (and not attached): [1] Biobase_2.8.0 BSgenome_1.16.0 grid_2.11.0 hwriter_1.2 [5] tools_2.11.0 XML_2.8-1 --------------------------------------------------------------------- SECURITY/CONFIDENTIALITY WARNING: \ This message an...{{dropped:24}}

On Thu, Apr 29, 2010 at 3:08 PM, Li, Xuejun <xueli@coh.org> wrote: > Hello everything, > > I have a question regarding the getTable function in the rtracklayer > package. The code below used to work in previous R version, but it > doesn't for the current release. I can't figure out what the problem is. > Can anyone give some hint? Thanks for your help! > > > > Best, > > > > Arthur Xuejun Li > > City of Hope Comprehensive Cancer Center > > Department of Information Science > > 1500 East Duarte Road > > Duarte, CA 91010 - 3000 > > Ph: (626) 256-4673 ext. 65121 > > Fax: (626) 471-7106 > > > > > > > > > session <- browserSession() > > > genome(session) <- "mm9" > > > foo <- trackNames(session)[trackNames(session) =="rmsk"] > > Why not just set foo to "rmsk"? > > bar<- ucscTableQuery(session, foo) > > > bar1 <- getTable(bar) > > Error in if (st[["status"]] == 100) { : > > missing value where TRUE/FALSE needed > > This look something is happening in RCurl. I won't be able to look into this for a couple of days, but do you know if your RCurl version changed along with rtracklayer? Thanks, Michael > > > > > > > > sessionInfo() > > R version 2.11.0 (2010-04-22) > > 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] stats graphics grDevices utils datasets methods base > > > > > other attached packages: > > [1] rtracklayer_1.8.1 RCurl_1.4-1 bitops_1.0-4.1 > > [4] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 > > [7] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 > > > > loaded via a namespace (and not attached): > > [1] Biobase_2.8.0 BSgenome_1.16.0 grid_2.11.0 hwriter_1.2 > > [5] tools_2.11.0 XML_2.8-1 > > > > > > > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message an...{{dropped:24}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]