matchprobes seems to be absent from the devel branch when I use R-2.12-alpha with biocLite? Perhaps this is a fluke because I have installed it earlier in the year under R-devel (then R-2.12), but it is also absent from the devel build webpage: http://bioconductor.org/checkResults/devel/bioc-LATEST/ Kasper
[Bioc-devel] matchprobes
3 messages · Hervé Pagès, Kasper Daniel Hansen
Hi Kasper,
On 09/19/2010 01:36 PM, Kasper Daniel Hansen wrote:
matchprobes seems to be absent from the devel branch when I use R-2.12-alpha with biocLite? Perhaps this is a fluke because I have installed it earlier in the year under R-devel (then R-2.12), but it is also absent from the devel build webpage: http://bioconductor.org/checkResults/devel/bioc-LATEST/
Yes matchprobes has been deprecated for a while (more than 2 releases
ago) and now it's gone. Note that at the same time we made it
a deprecated package, we also moved most of its content to Biostrings:
basecontent()
countbases()
complementSeq()
reverseSeq()
revcompDNA()
revcompRNA()
longestConsecutive()
matchprobes()
Most of this stuff is deprecated too. See the individual man pages
for the details.
Cheers,
H.
Kasper
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
Sure, Biostrings is the better place. I was wondering (caring) about the probe annotation packages but you seem to have moved the probetable functions (like print.probetable) into AnnotationDbi which looks fine as well. Thanks for the explanation, Kasper 2010/9/19 Herv? Pag?s <hpages at fhcrc.org>:
Hi Kasper, On 09/19/2010 01:36 PM, Kasper Daniel Hansen wrote:
matchprobes seems to be absent from the devel branch when I use R-2.12-alpha with biocLite? ?Perhaps this is a fluke because I have installed it earlier in the year under R-devel (then R-2.12), but it is also absent from the devel build webpage: ? http://bioconductor.org/checkResults/devel/bioc-LATEST/
Yes matchprobes has been deprecated for a while (more than 2 releases ago) and now it's gone. Note that at the same time we made it a deprecated package, we also moved most of its content to Biostrings: ? ?basecontent() ? ?countbases() ? ?complementSeq() ? ?reverseSeq() ? ?revcompDNA() ? ?revcompRNA() ? ?longestConsecutive() ? ?matchprobes() Most of this stuff is deprecated too. See the individual man pages for the details. Cheers, H.
Kasper
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: ?(206) 667-5791 Fax: ? ?(206) 667-1319