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

Error: pandoc document conversion failed with error 127

 system call failed: Cannot allocate memory 

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