[BioC] biocLite breaks when `svn rev` is "unknown"

[Martin Morgan]

On 10/22/2011 10:14 PM, Michael Lawrence wrote:
>
>
> On Sat, Oct 22, 2011 at 11:03 AM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 10/22/2011 08:33 AM, Michael Lawrence wrote:
>
>         This is what I get:
>
>             biocLite("TxDb.Hsapiens.UCSC.__hg19")
>
>         Error in if (svnRev<  55733) .stop("R-2.14 r55733 or newer
>         required.") :
>            missing value where TRUE/FALSE needed
>
>         My `svn rev` in Rversion() is "unknown". No idea why.  Maybe
>         it's just
>         really old and the computer forgot? Maybe a warning should be
>         issued, and
>         then continue?
>
>
>     Thanks Michael -- this should be fixed in BiocInstaller version
>     1.1.29; because the error is in your installed package, you'll
>     (currently) need to remove.packages("__BiocInstaller") before
>     source("http://bioconductor.__org/biocLite.R
>     <http://bioconductor.org/biocLite.R>"); biocLite(character()) or
>     whatever.
>
>
> Maybe the biocLite.R script could check for a newer version of
> BiocInstaller?

It does; there are some edge cases and I thought this might be one of 
them, offering remove.packages to hedge my bets. Martin

>
>     Martin
>
>
>             sessionInfo()
>
>         R version 2.14.0 Under development (unstable) (--)
>         Platform: i686-pc-linux-gnu (32-bit)
>
>         locale:
>         [1] C
>
>         attached base packages:
>         [1] stats     graphics  grDevices utils     datasets  methods   base
>
>         other attached packages:
>         [1] BiocInstaller_1.1.28 rtracklayer_1.13.19  RCurl_1.5-0
>         [4] bitops_1.0-4.1
>
>         loaded via a namespace (and not attached):
>         [1] BSgenome_1.21.3      Biostrings_2.21.11   GenomicRanges_1.5.49
>         [4] IRanges_1.11.27      XML_3.2-0            tools_2.14.0
>         [7] zlibbioc_0.1.6
>
>         Thanks,
>         Michael
>
>                 [[alternative HTML version deleted]]
>
>         _________________________________________________
>         Bioconductor mailing list
>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>         https://stat.ethz.ch/mailman/__listinfo/bioconductor
>         <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>         Search the archives:
>         http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>         <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>
>
>     --
>     Computational Biology
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>     Location: M1-B861
>     Telephone: 206 667-2793 <tel:206%20667-2793>
>
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793