[Bioc-devel] biocValid() and suggested solution

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

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 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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