Re: [BioC] Follow-up to: [R] Annotation metadata kills help.search
Gerard Tromp [EMAIL PROTECTED] writes: Greetings, this is a follow-up to the mailing below. Seth Falcon replied and indicated that he and several others were unable to replicate the problem. Specifically he requested: We are not able to reproduce this issue. If you reinstall the annotation packages does the error reappear? If so, an exact transcript of the commands entered, their output, and the output of traceback() right after the error would be helpful --- and it would be best to move the discussion to the bioconductor list. === The answers are: Yes, the problem is reproducible. I did a complete reinstall of R and bioconductor end everything worked fine until I installed an annotation package. With the added information from Gerard, we were able to reproduce the problem and are currently working on a fix. Thanks, + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [BioC] Follow-up to: [R] Annotation metadata kills help.search
Hello Gerard, all, The annotation packages breaking help.search was due to improperly built annotation packages. We have posted updated annotation packages to the Bioconductor meta data repository. Reinstalling the annotation data packages should resolve the issue and allow help.search to function normally. Please let us know (on [EMAIL PROTECTED]) if you find otherwise. Thanks, + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Annotation metadata kills help.search
Hi Gerard, Gerard Tromp [EMAIL PROTECTED] writes: OS: Windows R 2.0.1 As of about a week ago the help.search function dies when used in the simple help.search(something) usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 We (the Bioconductor team) will look into this and see if we can reproduce what you are reporting. This is the first we've heard of difficulties with the help system caused by the annotation data packages. + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Annotation metadata kills help.search
Seth Falcon [EMAIL PROTECTED] writes: Hi Gerard, Gerard Tromp [EMAIL PROTECTED] writes: OS: Windows R 2.0.1 As of about a week ago the help.search function dies when used in the simple help.search(something) usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 We (the Bioconductor team) will look into this and see if we can reproduce what you are reporting. This is the first we've heard of difficulties with the help system caused by the annotation data packages. We are not able to reproduce this issue. If you reinstall the annotation packages does the error reappear? If so, an exact transcript of the commands entered, their output, and the output of traceback() right after the error would be helpful --- and it would be best to move the discussion to the bioconductor list. + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Annotation metadata kills help.search
Greetings! OS: Windows R 2.0.1 Before anyone flames -- I tried to query this on the R searchable web site and using google and did not find anything applicable. As of about a week ago the help.search function dies when used in the simple help.search(something) usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 When I move these out of the library directory, help.search() functions correctly again. I have not tracked it any further -- just wanted to know if anyone else had noticed it. Gerard Tromp __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Annotation metadata kills help.search
This happened to me in R 2.1.0 (I forget which specific version since I now have March 27th) on Windows XP which I traced to package dataRep. Once I removed that package help.search worked again. On Mon, 28 Mar 2005 22:08:58 -0500, Gerard Tromp [EMAIL PROTECTED] wrote: Greetings! OS: Windows R 2.0.1 Before anyone flames -- I tried to query this on the R searchable web site and using google and did not find anything applicable. As of about a week ago the help.search function dies when used in the simple help.search(something) usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 When I move these out of the library directory, help.search() functions correctly again. I have not tracked it any further -- just wanted to know if anyone else had noticed it. Gerard Tromp __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
