Re: [Bioc-devel] New Team Member

Welcome Best, Kasper On Sun, May 8, 2016 at 9:48 AM, Martin Morgan wrote: > Bioc developers, > > We're very pleased to welcome Lori Shepherd to the Bioconductor team in > Buffalo. Lori has a Masters in Bioinformatics and Biostatistics. Her > background includes

Re: [Bioc-devel] GEOquery for Bioc devel

Thanks Sean! It looks like it does build and check. But the last commit was made after the daily deadline (4:20PM Seattle time) so this won't be available via biocLite() till Tuesday sometime. It can be installed via git or svn in the meantime. Dan - Original Message - > From: "Sean

Re: [Bioc-devel] GEOquery for Bioc devel

Hi, all. Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO switching to using https for GEO data tables. This is not a highly-used feature, but it was enough to break the build. It should be fixed (cross fingers) in Devel. If fixed in devel, I will backport to

[Bioc-devel] Mac builds in bioconductor devel

Hi all, You may have noticed that there are no Mac builds in the new devel (Bioconductor 3.4) build report. One of the build macs died. We have ordered replacement hardware and we hope it will arrive soon. Then after it is configured, we aim to get Mac builds going again as soon as

Re: [Bioc-devel] downloads number status shields for packages

Hi Wolfgang, Yep. All good suggestions. Thanks! H. On 05/08/2016 12:52 AM, Wolfgang Huber wrote: Hervé Thank you, looks great. Regarding files like https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats: woudln’t it be good to - provide column headers - give the file a

Re: [Bioc-devel] GEOquery for Bioc devel

GEOmetadb had an issue with Dropbox jerking around URLs (cf https://github.com/ttriche/simpleSampleSearch/blob/master/R/checkForUpdates.R ); I wonder if this might be related? I'd hate for GEO to become as flaky as biomaRt. I should have submitted simpleSampleSearch for 3.3 but it seemed too

Re: [Bioc-devel] GEOquery for Bioc devel

GEOquery is available in release (3.3), though not the most recent version. Hopefully release and not devel is being used in the edX class; the devel builds are not yet stable, but should be later today. In any case, it's early-cycle devel. Dan - Original Message - > From: "Dan

Re: [Bioc-devel] GEOquery for Bioc devel

Maybe. If the package does not build for many days on end, it's more than flakiness and one wonders if the service is usable at all. Tests that indicate this seem appropriate to me, though I agree false positives can be annoying. Dan - Original Message - > From: "Vincent Carey"

Re: [Bioc-devel] GEOquery for Bioc devel

Hmm. Very important piece of software so we should try to remedy this. I had assigned some GEOquery problems in the edX class and there were some people who could not get getGEO to work, but the problem seemed intermittent. There was a workaround posted on the support site which involved

Re: [Bioc-devel] GEOquery for Bioc devel

It has not built since the devel (3.4) builds started. Apparently GEO has been pretty flaky. Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Sunday, May 8, 2016 5:54:59 AM > Subject:

[Bioc-devel] New package submission process

New package developers -- We hope to start the new package submission process https://support.bioconductor.org/p/76472 as early as May 23, 2016. If you're planning to submit packages to Bioconductor after that date, please develop your package using a github repository; we'll use these as

[Bioc-devel] New Team Member

Bioc developers, We're very pleased to welcome Lori Shepherd to the Bioconductor team in Buffalo. Lori has a Masters in Bioinformatics and Biostatistics. Her background includes sequence analysis, server administration, and R package development. You might already have seen Lori getting up to

Re: [Bioc-devel] downloads number status shields for packages

Hervé Thank you, looks great. Regarding files like https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats: woudln’t it be good to - provide column headers - give the file a reasonable extension reminding of its format - format it such that it can be read with default