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

[Dan Tenenbaum]

Hi,

The problem on linux has been fixed, but now there's another problem. It is running out of memory when building your workflow.

The problem on mac is that R-3.2.x is not compatible with the newest knitr (1.13), so the recommendation is to downgrade to knitr 1.12 or upgrade to R-3.3.0.
The workflow builders will update to R-3.3.0 soon, so this issue will go away then.

In the meantime, I did try and downgrade the machine to knitr 1.12 but the workflow build code rightfully updated everything before building so that had no effect.

Both of these new build results are here:

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/8/

Dan


----- Original Message -----
> From: "Bernd Klaus" <bernd.klaus at embl.de>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, May 23, 2016 3:33:24 AM
> Subject: [Bioc-devel] workflow builds on windows but not on mac and linux

> 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
> 
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