[R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package

[Duncan Murdoch]

On 15/04/2020 5:14 a.m., Paul SAVARY wrote:
> Hello,
> 
> I'm having trouble re-submitting a package (graph4lg).
> 
> - With r-patched_osx, vignette rebuilding fails with the following message :
> 
> checking re-building of vignette outputs ... [12s/16s] WARNING
> Error(s) in re-building vignettes:
> ...
> --- re-building ‘vignette_graph4lg.Rmd’ using rmarkdown
> dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
> Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
> Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ____chkstk_darwin
> Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
> Expected in: /usr/lib/libSystem.B.dylib
> 
> Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics:
> pandoc document conversion failed with error 6
> --- failed re-building ‘vignette_graph4lg.Rmd’
> 
> SUMMARY: processing the following file failed:
> ‘vignette_graph4lg.Rmd’
> 
> Error: Vignette re-building failed.
> Execution halted

I was told this was a transient problem on the MacOS build system:  the 
pandoc installed there was defective.  I don't know if it has been fixed 
yet.

> 
> - Besides, although I removed some unused packages from the imports in DESCRIPTION file, I still obtain this message :
> 
> checking dependencies in R code ... NOTE
> Namespaces in Imports field not imported from:
> ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’
> All declared Imports should be used.
> 
> Except Rdpack which is needed to build the vignette, I removed these packages.

Generally something needed only for the vignettes should be in Suggests 
rather than Imports.

> Finally, although I submit version 0.4.0, I receive checking errors relative to version 0.3.0.

It sounds like someone slipped up.  It might have been you (sending the 
wrong file, or looking at the wrong check log), or maybe CRAN.  In 
either case, I don't think there's anything you can do other than check 
that you're submitting the right file (use a new version number) after 
fixing the Rdpack issue.

Duncan Murdoch
> 
> I thank you in advance for your feedbacks.
> Regards
> Paul Savary
> 
> 
> 
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