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

Robert Castelo robert.castelo at upf.edu
Mon Sep 6 11:38:09 CEST 2010

dear developers,

i have the following lines in the main help page
(man/qpgraph-package.Rd) of my package 'qpgraph':

  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
  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 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


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).


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