[Bioc-devel] packageDescription() call in help page with recent R devel

[Martin Morgan]

On 09/06/2010 02:38 AM, Robert Castelo wrote:
> dear developers,
>
> i have the following lines in the main help page
> (man/qpgraph-package.Rd) of my package 'qpgraph':
>
> \details{
>   \tabular{ll}{
>   Package: \tab qpgraph\cr
>   Version: \tab \Sexpr{packageDescription("qpgraph")[["Version"]]}\cr
>   Built: \tab \Sexpr{packageDescription("qpgraph")[["Built"]]}\cr
>   Depends: \tab \Sexpr{packageDescription("qpgraph")[["Depends"]]}\cr
>   Imports: \tab \Sexpr{packageDescription("qpgraph")[["Imports"]]}\cr
>   Suggests: \tab \Sexpr{packageDescription("qpgraph")[["Suggests"]]}\cr
>   biocViews: \tab
> \Sexpr{packageDescription("qpgraph")[["biocViews"]]}\cr
>   License: \tab \Sexpr{packageDescription("qpgraph")[["License"]]}\cr
>   URL: \tab \Sexpr{packageDescription("qpgraph")[["URL"]]}\cr
>   }
> }
>
>
> so far i have been developing with the following development version of
> R:
>
> R version 2.12.0 Under development (unstable) (2010-06-30 r52417)
>
> under which the currently available version of the package runs without
> errors the R CMD build, R CMD check and R CMD INSTALL commands:
>
> however, in the daily build at the bioconductor site the follow error
> occurs:
>
> http://bioconductor.org/checkResults/2.7/bioc-LATEST/qpgraph/lamb2-buildsrc.html
>
> Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD build qpgraph
> StartedAt: 2010-09-05 02:17:17 -0700 (Sun, 05 Sep 2010)
> EndedAt: 2010-09-05 02:17:25 -0700 (Sun, 05 Sep 2010)
>
> * checking for file ‘qpgraph/DESCRIPTION’ ... OK
> * preparing ‘qpgraph’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * running cleanup
> * installing the package to process help pages
> * building the package manual
> Hmm ... looks like a package
> Converting Rd files to LaTeX ..Warning in packageDescription("qpgraph") :
>   no package 'qpgraph' was found
> Error : /loc/home/biocbuild/bbs-2.7-bioc/meat/qpgraph/man/qpgraph-package.Rd:9: subscript out of bounds
>
>
> where the following development version of R is employed:
>
> 2.12.0 Under development (unstable) (2010-08-26 r52817)
>
> i have updated my development version to the lates one and indeed i can now reproduce
> the error when doing R CMD build.
>
> therefore, something changed in the R development version since june that now it does not accept anymore
> to have 'packageDescription()' calls in '\Sexpr{}' tags within help pages.
>
> i have been googling a bit, and looking to the documentation whether there is any update about the use of
> 'packageDescription()' but so far i have not found anything.
>
> does anyone know if this is an intended change?
>
> if yes, do you think is there any workaround?
>
> if not, and this is therefore a bug, how do you recommend me to report it? (i'd appreciate if maybe some
> core R-developer here would do it for me).
>   

I'll ask on R-devel and report back if this is resolved. Martin
> thanks!!
> robert.
>
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