Re: [Bioc-devel] workflow builds on windows but not on mac and linux
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" > > To: "bioc-devel" > > 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
Re: [Bioc-devel] workflow builds on windows but not on mac and linux
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" > To: "bioc-devel" > 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
[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
