Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Hi guys, - this is a very interesting discussion, and thanks for sharing your ideas. On a maybe relevant note, during my previous effort trying to create an alternative workflow auto-build system based on Docker containerization using my package liftr, I found some similar issues in declaring

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

I haven't tried (= had to do it) myself, so I don't know exactly what it takes, but you can configure this "ulimit" of number of open files, e.g. instructions in https://stackoverflow.com/a/34645/1072091. I suspect it requires admin rights, but I'm not sure - maybe this is what goes on when you

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Interesting! In iTerm2, I get $ ulimit -Sn 4864 and env R_MAX_NUM_DLLS=1000 R works, which means that on Mac it IS possible to have many more DLLs open than 100 if R is started in the right way. Wolfgang PS I meant OS X 10.12.6, too. SOrry for the typo. 6.10.17 14:50, Kasper Daniel Hansen

[Bioc-devel] Bioconductor 3.6 release: new package deadline

Hello, Today Friday October 6 is the deadline for new package submissions for a chance to be included in Bioc 3.6. Packages submitted before this date, the core will try and work with to get the package through the acceptance process before the deadline. Packages submitted after this date will

[Bioc-devel] Bioconductor 3.6 release: db0 annotations

Hi, The new db0 packages, version 3.4.3, are now available in the devel branch, e.g., http://www.bioconductor.org/packages/devel/data/annotation/html/human.db0.html Let us know if you run into problems. The plan is to make the new OrgDbs available next Friday, October 13, so feedback about

Re: [Bioc-devel] BIOC devel 3.6 buid/check

sorry ... please check the results of git remote -v to make sure the upstream remote is set. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] BIOC devel 3.6 buid/check

Did you set the upstream remote? The upstream remote should be g...@git.bioconductor.org:packages/maSigPro.git git remote add g...@git.bioconductor.org:packages/maSigPro.git will set this. what do you see when you do remote -v? If that is set... Did you remember to git push upstream

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

On OS X 10.12.6 (I don't think 10.12.16 exists), I get $ ulimit -Sn 7168 Interestingly, this is because I use iTerm2 for my command line prompt. If I do the same command in Terminal I get 256. If I start R inside of Emacs I get 256 as well. I don't know anything about ulimit and how it is

Re: [Bioc-devel] Duplicate commit error on and off

This is good news! > On Oct 5, 2017, at 7:06 PM, Thomas Girke wrote: > > Thanks. I have synced everything to the current development and was able to > commit back to Bioc-upstream/master. > > Thomas > > On Thu, Oct 5, 2017 at 10:28 AM Turaga, Nitesh >

Re: [Bioc-devel] Problem building package with devtools+Rcpp

Thank you Morgan, this is indeed working Quoting Martin Morgan : > On 09/27/2017 08:11 AM, sergi.pic...@upc.edu wrote: >> Dear developers, >> Sorry if the e-mail is duplicated, I had an issue sending it. >>       I have been struggling with problems building my

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

On Mac OSX 10.12.16: $ ulimit -Sn 256 so the maximum value of R_MAX_NUM_DLLS is 153 ... Wolfgang 5.10.17 23:02, Henrik Bengtsson scripsit: About the DLL limit: Just wanna make sure you're aware of "new" environment variable R_MAX_NUM_DLLS available in R (>= 3.4.0). It allows you to