[Bioc-devel] GateFinder: Windows Server Error

Hello, I'm working on resolving the error with the GateFinder package for Windows Server 2012 R2 Standard, it appears that the issue is a calculation difference between 32 and 64-bit systems. Is it possible to have the package be included in the next release only with support for 64-bit systems?

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Dear Michael, Thanks, that fixed the problem. The new version hasn’t shown up in a call to biocLite, but I was able to get it from the github repository and check it; also our package is now clearing bioconductor checks. Just to note, our package has always gotten messages about the class

Re: [Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

Hi again, I just had a thought. Would it be possible to extend the citation pages that you linked to also provide the bibtex source at a similar URL, e.g. http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/bibtex.html

Re: [Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

I wasn't specific about what I meant by "structured" because I'm not certain what kind of citation data types CiteAs can handle, though I'd assume bibtex would probably be fine. It's possible that the unprocessed CITATION file might also be good enough (I'm not familiar with the format). On Tue,

[Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

Hi Ryan, Thanks for pointing this out. I'm not sure what you mean by "structured" or "format". We do have public facing citations which can be found at: http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html (Thanks Lori for locating these pages!) And even with a

[Bioc-devel] TxDbs, OrgDbs, GO.db, and PFAM.db packages available

Hello all! The newest TxDbs, OrgDbs, GO.db, and PFAM.db packages have been pushed to Bioconductor 3.7 devel and should propagate by tomorrow. The following packages have been updated/added: Updated GO.db: GO.db_3.6.0.tar.gz Updated PFAM.db: PFAM.db_3.6.0.tar.gz Updated org dbs:

[Bioc-devel] Transition from Google Sheet to Web App

Hi developers, Tomorrow we are bringing a web app online to help with the management of SSH keys. The app will replace the Google Sheet currently used to add keys. Through the web interface you'll be able to add keys and change your email or github username. There is also an option to see what

[Bioc-devel] Accessing package citation info programmatically without running R?

There's a nice online tool called CiteAs which tries to figure out the proper citation for a given URL. I've recently helped the author to add support for extracting the DOI from Bioconductor package information pages: https://github.com/Impactstory/citeas-api/issues/12 This is a good start, but

Re: [Bioc-devel] RareVariantVis failed

I just checked and it is indeed updated on the git.bioconductor.org server. So you should be all set. The version number in the build report should be updated either tomorrow or thur to indicate it is building the new 2.7.1 version of the package.

Re: [Bioc-devel] RareVariantVis failed

Yes that is correct. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Tomasz Stokowy Sent: Tuesday, April 17, 2018

Re: [Bioc-devel] RareVariantVis failed

You need to push the changes to the git.bioconductor.org server. What is the result of `git remote -v` You should have set up the upstream remote to point the the Bioconductor git server where you will also have to push changes. See the following help page:

Re: [Bioc-devel] RareVariantVis failed

Ok, I pushed to upstream master. Where could I check that version "to be checked" was updated to 2.7.1? -- Tomasz On Tue, 17 Apr 2018 17:35:18 +0200, Shepherd, Lori wrote: Yes that is correct. Lori Shepherd Bioconductor Core Team Roswell Park Cancer

Re: [Bioc-devel] RareVariantVis failed

Output of git remote -v seems to be ok: Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v origin https://github.com/tstokowy/RareVariantVis.git (fetch) origin https://github.com/tstokowy/RareVariantVis.git (push) upstream g...@git.bioconductor.org:packages/RareVariantVis.git

[Rd] Minor glitch in optim()

Having worked with optim() and related programs for years, it surprised me that I haven't noticed this before, but optim() is inconsistent in how it deals with bounds constraints specified at infinity. Here's an example: # optim-glitch-Ex.R x0<-c(1,2,3,4) fnt <- function(x, fscale=10){ yy <-

Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

Yes, thanks. That also fixed it for me; only DelayedArray had a different version number. I have 0.17.42 of S4Vectors because there were also a fix in that package that I need which are also not yet available from bioCLite (the question of duplicated class names creating messages was breaking

Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

Hi Elizabeth, Aaron and I were hit by this same error message. As a workaround, installing DelayedArray and HDF5Array from the git(hub) repo fixed the issue (https://github.com/Bioconductor/HDF5Array/issues/6). But this needs to be propagated to the versions made available via BiocLite().

[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

Hello, When I try to run the example code in the saveHDF5SummarizedExperiment function, I get the error "Error: C stack usage 7969416 is too close to the limit”. I am working with development R and have incorporated HDF5 functionality in my package. I did so many weeks ago on earlier versions

Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

Hi Shijia, I guess you should update the dependency from 2.15 to 3.5. In the DESCRIPTION file add R 3.5 as dependency: Depends: R (>= 3.5) This should fix the warning. Carmen On 17/04/2018 10:49, Shijia Zhu wrote: Hi Everyone, I submitted my package to Bioconductor, but always meet with

Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

You had the right idea with your commit https://github.com/zhushijia/GIGSEA/commit/431af209590f905452b5f10b0ad3a282ab2534e3 but the wrong version of R. You need to put Depends: R (>= 3.5) in your DESCRIPTION file and it should be good. Mike On 17 April 2018 at 10:49, Shijia Zhu

Re: [Rd] strange warning: data() error?

> On 17 Apr 2018, at 01:08 , David Winsemius wrote: > > > Hypothesis: datasets in a ..library/data/Rdata.rds file whose listing does > not match the name of the dataset from which it is derived will cause the > behavior in question. Yes, because data() originally

Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

Hi Everyone, I submitted my package to Bioconductor, but always meet with the following warning: ** Checking R Version dependency...* WARNING: Update R version dependency from 2.15 to 3.5.* Does anyone know how to fix the warning? Any help will be appreciated very much. Best Shijia

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

Dear Alex, Have a look at drat (http://eddelbuettel.github.io/drat/DratForPackageAuthors.html). This makes it easier to distribute prepackaged R packages (including When you uploaded a new version, then the student would only have to do drat::addRepo("your_repo") and then