[Bioc-devel] biocValid() and suggested solution

[Martin Morgan]

Actually, biocValid was following the convention in R of using the function 
sQuote(<...>) to 'quote' package names, e.g.,

   install.packages("sfdsdfs")

which eventually tells us

   Warning message:
   package 'sfdsdfs' is not available (for R version 3.0.0 Patched)

with fancy quotes. The right thing to do is to

   options(useFancyQuotes = FALSE)

which I have in my ~/.Rprofile.

Martin

On 04/26/2013 10:21 AM, Dan Tenenbaum wrote:
> 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
>>
>>
>
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>


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