[Rd] Log file of building vignette in RCMD check

[Stefan McKinnon Høj-Edwards]

Hello,

I am trying to run "RCMD check" on a package. It performs OK, with the exception of a single warning:
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   AnnotationFuncsUserguide.Rnw

As I understand the problem, the vignette is not built. However, I have no problems in doing so manually.
How do I fix this problem? I cannot find any logs for building the vignette, however the output from building the pdf-file of the manual is found in the .Rcheck folder. 

On a similar note, as my vignette includes a biblio, I have to run "latex" twice to get the citations referenced properly with a number. Is this an issue? How can I work around it? (The package is submitted to BioC, so there might be other rules there?)

Thank you in advanced.
Yours sincerely,

Stefan McKinnon Høj-Edwards     Dept. of Genetics and Biotechnology
PhD student                     Faculty of Agricultural Sciences
stefan.hoj-edwards at agrsci.dk    Aarhus University
Tel.: +45 8999 1291             Blichers Allé 20, Postboks 50
Web: www.iysik.com              DK-8830 Tjele
                                Tel.: +45 8999 1900
                                Web: www.agrsci.au.dk