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Question: rtracklayer - getTable
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gravatar for Michael Lawrence
7.6 years ago by
United States
Michael Lawrence9.8k wrote:
Just FYI, I've been able to reproduce this, and the maintainer of RCurl is looking into the issue. Michael On Fri, Apr 30, 2010 at 4:28 AM, Li, Xuejun <xueli@coh.org> wrote: > Michael, > Thanks for your reply. Actually I didn't notice the change. I will take a > look next Monday. > > Best, > Arthur > > ------------------------------ > *From:* Michael Lawrence [mailto:lawrence.michael@gene.com] > *Sent:* Fri 4/30/2010 4:26 AM > *To:* Li, Xuejun > *Cc:* bioconductor@stat.math.ethz.ch > *Subject:* Re: [BioC] rtracklayer - getTable > > > > 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]]
ADD COMMENTlink written 7.6 years ago by Michael Lawrence9.8k
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