[Bioc-devel] workflow builds on windows but not on mac and linux

[Bernd Klaus]

Dear all,

I recently took up developing a workflow again (matEndToEnd). 

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/

While it builds fine on windows (winbuilder1) I get error message on
linux (master) and mac (vagrantmac) that I cannot really trace down.

1.) On vagrantmac, it gives 


> * creating vignettes ... ERROR
> Quitting from lines 36-43 (MA-Workflow.Rmd) 
>  Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
> unused arguments (filename, stop_on_error != 2)

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=vagrantmac/lastBuild/console


Some searching revealed that this might be related to using a version
of knitr that is too old:

http://stackoverflow.com/questions/37241578/getting-a-parser-all-error-in-r-when-using-knitr-for-converting-a-basic-rmd-file

  
2.) On master the error is:


> * installing the package to build vignettes
> * creating vignettes ... ERROR
> Error : .onLoad failed in loadNamespace() for 'BiocInstaller', details:
>   call: url(paste0(.protocol(), "//bioconductor.org/BiocInstaller.dcf"))
>   error: https:// URLs are not supported
> Quitting from lines 76-109 (MA-Workflow.Rmd) 

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=master/lastBuild/console


potentially "old" package versions are a problem here as well?

(All servers still seem to still use Bioc 3.2 in principle, but 
maybe there is some mixup between old and new? )


Thanks a lot and best wishes,

Bernd