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

[Bernd Klaus]

Hi Dan,

thanks a lot for your prompt response! 

Do you have any idea how I could possibly trace down the memory issue on
Ubuntu?

I commented the sessionInfo() chunk at the end of the workflow and now I
get on "master"

> Error: pandoc document conversion failed with error 127
and
>  system call failed: Cannot allocate memory 

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=master/9/console

- which might be related to some system settings in Ubuntu:
http://stackoverflow.com/questions/27136264/unable-to-install-packages-system-call-failed-cannot-allocate-memory-instal

Thanks again and best wishes,

Bernd

PS; I can compile the workflow on a 8 GB RAM ubuntu  (15.10, latest R,
Bioc 3.3.) laptop locally. 

On Mo, 2016-05-23 at 14:53 -0700, Dan Tenenbaum wrote:
> 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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