[Bioc-devel] Question about sumbition process and biocviews

[Ioannis Vardaxis]

Hi,

I was Rechecking the  package folder and not the built version. Now it
works, thanks.


The warning I get for the references is the following:
Warning in parse_Rd(manpage) :
  
/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/sum
mary.Rd:78: unknown macro '\insertRef'




-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU




On 07/11/16 02:36, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:

>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: ³From R version >=3.2 vignettes is
>>required
>> to be placed in /inst/doc²
>
>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 don¹t then Rcheck
>>gives
>> an error. If I place vignettes in /inst/doc then Rcheck checks it
>>without
>> any error.
>>
>>
>
>
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