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

Bernd Klaus bernd.klaus at embl.de
Mon May 23 12:33:24 CEST 2016

Dear all,

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


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)


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


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) 


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,


More information about the Bioc-devel mailing list