Re: [Bioc-devel] missing link for BiocParallel_1.16.2.tar.gz

2019-01-04 Thread Martin Morgan
You caught the pages during updates -- after the nightly build the current release available via biocLite() and at the endpoint for the url was 1.16.4, but the 'landing page' was presenting links from before the update. The reasons for the lag are several, including local caching by your

[Bioc-devel] missing link for BiocParallel_1.16.2.tar.gz

2019-01-04 Thread Lorsung, Michael J. via Bioc-devel
Hello bioconductor support people and users, On http://master.bioconductor.org/packages/release/bioc/html/BiocParallel.html the source package link is not working (near bottom of page) Source Package

Re: [Bioc-devel] Memory usage for bplapply

2019-01-04 Thread Martin Morgan
Memory use can be complicated to understand. library(BiocParallel) v <- replicate(100, rnorm(1), simplify=FALSE) bplapply(v, sum) by default, bplapply splits 100 jobs (each element of the list) equally between the number of cores available, and sends just the necessary data

Re: [Bioc-devel] SSH keys for the newly accepted package RCM

2019-01-04 Thread Obenchain, Valerie
Hi Joris, This query was also sent to Bioconductor/Contributions on github. I've responded there. Valerie On 1/4/19 6:23 AM, Joris Meys wrote: > Dear, > > I'm the maintainer of the new package RCM, written by Stijn Hawinkel. In > the issue on github Stijn was asked to submit a SSH key to

[Bioc-devel] List of Deprecated Package Bioc 3.9

2019-01-04 Thread Shepherd, Lori
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.9 is as follows: **Maintainer requested

[Bioc-devel] SSH keys for the newly accepted package RCM

2019-01-04 Thread Joris Meys
Dear, I'm the maintainer of the new package RCM, written by Stijn Hawinkel. In the issue on github Stijn was asked to submit a SSH key to Bioconductor ( https://github.com/Bioconductor/Contributions/issues/949#issuecomment-451232446 ). I am also the maintainer of the unifiedWMWqPCR package and

[Bioc-devel] devel software builds

2019-01-04 Thread Obenchain, Valerie
malbec2 stopped building last night around 9pm EST. I'm not sure yet what happened - looks like a network issue. Just a heads up that today's report will only include Mac and Windows. Valerie This email message may contain legally privileged and/or confidential information. If you are not

[Bioc-devel] package download stats

2019-01-04 Thread Obenchain, Valerie
We've been having problems with the machine that runs the download stats so results haven't been posting regularly. This was fixed earlier this week and new results should all post today. Software is already done, annotation is in progress ... Valerie This email message may contain legally

Re: [Bioc-devel] Travis CI errors for BiocManager

2019-01-04 Thread Martin Morgan
This is fixed in r75946 https://stat.ethz.ch/pipermail/r-devel/2019-January/077155.html Martin On 1/3/19, 12:06 PM, "Erik Fasterius" wrote: Ah, okey! Very good to know, thank you! Is there a way I can keep track of this, to see when it gets fixed? Erik > On 3 Jan 2019,

Re: [Bioc-devel] Controlling vignette compilation order

2019-01-04 Thread Aaron Lun
Thanks for the update Martin. At least separate processes will avoid the MAX_DLL problems we had earlier. “simpleSingleCell” is now set up so that each vignette will try to compile any upstream vignettes that it depends on (if those upstream targets haven’t already been built). This is done in