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.kl...@embl.de> > > To: "bioc-devel" <bioc-devel@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 > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
