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

2016-05-24 Thread 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

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

2016-05-23 Thread 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

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

2016-05-23 Thread Bernd Klaus
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