[Bioc-devel] biocValid() and suggested solution

[Dan Tenenbaum]

On Fri, Apr 26, 2013 at 9:58 AM, Diego Diez <diez at kuicr.kyoto-u.ac.jp> wrote:

> Hi all,
>
> trying to solve a screw with my bioconductor installation I found the
> very useful function biocValid(). Unfortunately the suggested action
> to downgrade my installation is shown with curly double quotes that
> prevents to just copy/paste the command, making it slightly less
> practical (had to paste it into an editor to find/replace =93 and =94 with
> "). For example:
>
> downgrade with biocLite(c(=93annotate=94, =93AnnotationDbi=94,
> =93AnnotationForge=94, =93Biobase=94,
>   =93BiocGenerics=94, =93BiocInstaller=94, =93biomaRt=94, =93Biostrings=94,=
>  =93BSgenome=94,
>   =93Category=94, =93codelink=94, =93edgeR=94, =93genefilter=94, =93Genomic=
> Ranges=94, =93GOstats=94,
>   =93graph=94, =93GSEABase=94, =93IRanges=94, =93limma=94, =93motifStack=94=
> , =93MotIV=94, =93PWMEnrich=94,
>   =93RBGL=94, =93rGADEM=94, =93seqLogo=94))
>
> rather than:
>
> downgrade with biocLite(c("annotate", "AnnotationDbi",
> "AnnotationForge", "Biobase",
>   "BiocGenerics", "BiocInstaller", "biomaRt", "Biostrings", "BSgenome",
>   "Category", "codelink", "edgeR", "genefilter", "GenomicRanges", "GOstats"=
> ,
>   "graph", "GSEABase", "IRanges", "limma", "motifStack", "MotIV", "PWMEnric=
> h",
>   "RBGL", "rGADEM", "seqLogo"))
>
> Is this intentional or could this aspect be improved?
>


This is fixed in BiocInstaller 1.10.1 and 1.11.1, which will be
available via biocLite() late tomorrow morning Seattle time.

Thanks for pointing out this issue.
Dan



> Thank you,
> Diego
>
>
> --
> Diego Diez, PhD
> Assistant Professor
> Bioinformatics and Genomics Laboratory,
> WPI Immunology Frontier Research Center (IFReC)
> 8F Integrated Life Science Building, Osaka University,
> 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
> Phone: +81-6-6879-4266
> Fax: +81-6-6879-4272
> diez at ifrec.osaka-u.ac.jp
>
>