On 11/06/2016 06:10 PM, Ioannis Vardaxis wrote:
Hi,
For the references I just used @references \insertRef{key}{pkg}, and
although it shows up in the ??pkg::function help, I get an error in
biocCheck
it's not enough to say that you got an error, because there are many
possible errors. What error did you get?
For the vignettes, my vignette is generated without any errors. What I get
as en error in Rcheck is that: “From R version >=3.2 vignettes is required
to be placed in /inst/doc”
If I build and then check the package here
https://github.com/mtmorgan/PkgA/tree/no-vignette-engine
I see first of all during build that it does NOT say that it is loading
the package to build the vignette
$ R CMD build PkgA
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'
and then when I check the built package I see
$ R CMD check PkgA_0.0.1.tar.gz
...
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'vignette.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
The example package is missing the following lines in the vignette
---
vignette: >
%\VignetteIndexEntry{Short title for my vignette}
%\VignetteEngine{knitr::rmarkdown}
---
and the following field in the DESCRIPTION file
VignetteBuilder: knitr
If I add these, I see during package build that the vignette is being
built 'creating vignettes ... OK'
$ R CMD build PkgA
Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
* checking for file 'PkgA/DESCRIPTION' ... OK
* preparing 'PkgA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'PkgA_0.0.1.tar.gz'
and I do not see any vignette-related problems when I check the newly
built vignette.
It is more helpful to cut and paste the message from R CMD check
directly, perhaps with a translation, because the message often contains
infromation that an approximate message does not convey, e.g., that my
vignette uses R markdown. The solution to your problem might be slightly
different if you are using an Rnw-based vignette.
But if I do that the bioCheck gives an error, if I don’t then Rcheck gives
an error. If I place vignettes in /inst/doc then Rcheck checks it without
any error.
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