Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster

Hi Pariksheet, On 11/15/2016 03:32 AM, Pariksheet Nanda wrote: > Hi folks, > > It would be great to have an OrganismDb package for > Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and > Rattus.norvegicus. > > While trying to do this on my own using the Homo.sapiens package as a >

Re: [Bioc-devel] Error in DESeq Installation

Hi, I'm not having problems installing DESeq with Bioconductor 3.4 and R 3.3.1. Please try installing the package in a fresh R session, show the commands you ran and the output of sessionInfo(). Here's mine: > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit)

Re: [Bioc-devel] svn repository for proFIA/plasFIA maintainer

The RoswellPark IT dept would not let this message through because of the 'no release' in the title. I've removed that so the message can (hopefully) get through ... Valerie On 10/25/2016 06:46 AM, Obenchain, Valerie wrote: > Hi Alexis, > > Instructions for working with the diff

Re: [Bioc-devel] Package "not supported" on some platforms, and dependent packages

Just fyi, as stated in the NEWS, ensemblVEP >= 1.12.0 is not supported on windows because the Ensembl VEP tool >= 84 requires tabix. Valerie On 10/18/2016 04:01 PM, Kevin RUE wrote: > Agh, I could have looked better in the Git mirror code ;) > > Anyway, thanks a lot for the tip! > > No

Re: [Bioc-devel] maftools build error

Hi Anand, Looks like maftools is clean on the Oct 12 report: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ We've had some hiccups ... and it looks like that problem is transient. You can safely ignore it for now. Thanks for keeping an eye on the build report. Valerie On

Re: [Bioc-devel] RMassBank build error

Hi Emma, Yes, there is leeway for working on the package. Thank you for actively trying to fix it! Unfortunately the notification emails stopped (broke) at some point this dev cycle - we plan to reinstate them after the release on the new build machines. Thanks for your patience. Valerie On

[Bioc-devel] OrgDbs for Bioconductor 3.4

The OrgDb packages have been updated and are available in the devel branch. All have been bumped to version 3.4: org.Ag.eg.db org.At.tair.db org.Bt.eg.db org.Ce.eg.db org.Cf.eg.db org.Dm.eg.db org.Dr.eg.db org.EcK12.eg.db org.EcSakai.eg.db org.Gg.eg.db org.Hs.eg.db org.Mm.eg.db org.Mmu.eg.db

[Bioc-devel] TxDbs for Bioconductor 3.4

The TxDbs for Bioconductor 3.4 are built and available in the devel branch. One new package has been added (version 3.4): TxDb.Ptroglodytes.UCSC.rheMac8.refGene These packages are live tracks and have been updated (bumped to version 3.4): TxDb.Celegans.UCSC.ce11.refGene

Re: [Bioc-devel] unit test results not showing up for BridgeDbR?

Looks like you forgot to bump the version. These are the last commits: r121440 | e.willighagen | 2016-09-27 04:58:02 -0700 (Tue, 27 Sep 2016) | 1 line Changed paths: M /trunk/madman/Rpacks/BridgeDbR/DESCRIPTION I've

[Bioc-devel] Bioconductor 3.4 annotation packages

Annotation package contributors, The release of Bioconductor 3.4 is October 18 and the deadline for contributed annotations is October 13. See the full release schedule here: http://www.bioconductor.org/developers/release-schedule/ The new db0 packages are in devel and ready for use; all have

Re: [Bioc-devel] How to update annotation packages

Hi Jo, If you make the updated packages available via drop box and I can post them for you. Thanks for pointing out that we don't have web documentation on how to update annotations - I'll add some. Valerie On 09/16/2016 01:14 AM, Rainer Johannes wrote: > Dear all, > > I wanted to update the

Re: [Bioc-devel] Does Bioconductor update my DESCRIPTION automatically?

You need to bump the 'z' of the x.y.z version when you check in (svn log shows no version bump). This increment is a trigger for the package to be (re)built and propagated to the landing page. Currently the builds run Saturday, Monday and Wednesday at 7:15 pm PST. Reports are generated about 32

Re: [Bioc-devel] bioc AMI: permissions in R-libs

Hi Simon, Yes, this is a known problem. I will fix this for the Bioc 3.3 and 3.4 AMIs and will post back when it's done. Valerie On 08/24/2016 04:45 AM, Simon Anders wrote: > Hi > > I'm currently working with the Bioconductor Amazon Machine Instance > (AMI) for Bioc 3.3 (ami-64d43409) and

Re: [Bioc-devel] package not available (for R version 3.2.3)

Hi Etienne, The BiocInstaller package, which contains the biocLite() function, looks in different Bioconductor repositories depending on what version of R is being run. BiocInstaller 1.20.* (your code below) was looking in the previous release repository (Bioconductor 3.1 and R 3.2) where the

Re: [Bioc-devel] bioconductor/metabolomics Docker image available

Hi Steffen, On 07/27/2016 09:11 AM, Dan Tenenbaum wrote: > > - Original Message - >> From: "Steffen Neumann" >> To: "Dan Tenenbaum" >> Cc: "bioc-devel" >> Sent: Wednesday, July 27, 2016 5:02:22 AM >> Subject:

Re: [Bioc-devel] Experimental data package or ExperimentHub

ut it's also giving the "not found" error. > > save(get(sample.name[i]), file=paste0(sample.name[i],".rda")) > > > thanks > Mike > > On Thu, Jun 30, 2016 at 6:41 PM, Obenchain, Valerie > <valerie.obench...@roswellpark.org> wrote: >> Hi Mike, >

Re: [Bioc-devel] Experimental data package or ExperimentHub

Hi Mike, Yes, let's go the ExperimentHub route. The focus is on detailed documentation / real use cases so the vignette you describe sounds like a good fit. Essentially you'll put a package together that is very similar to an experimental data package with a few extra files described in the

Re: [Bioc-devel] Build ERRORS caused by unable to be find dependencies

Hi Marcin, Dan is out for a few days and can give a more detailed answer when he's back. This looks like a problem on our end with the windows builder. Several other packages are failing with similar error messages, re: missing dependencies on packages that successfully built. Thanks for

Re: [Bioc-devel] submitting annotation and data package

Hi, Historically annotation packages were not reviewed in the package tracker. Last year I starting asking authors to upload the package to a S3 bucket and open an issue on the package tracker (with no upload). I reviewed the package and posted comments to the tracker. This kept all communication

[Bioc-devel] New Package Submission Process

Package developers, On June 6 we will transition to our new 'package tracker' on github. The new system will enable a more public review process where community members (not just the assigned reviewer) can give technical and scientific input during the review. More background in this post:

Re: [Bioc-devel] Pushing updates in the release branch

Hi Charles, Yes, the usual advice is that you touch release for bug fixes only but can update as often as you like in devel. This is the same pattern followed for our experimental data and annotation packages. Once we have a release those data are frozen and for 6 months are considered the

Re: [Bioc-devel] select(Homo.sapiens,...) failing

Hi Vince, You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing check because of the biomart problems so you'll have to get it from svn. Let me know if you still have problems after updating. Val On 05/02/2016 11:53 AM, Vincent Carey wrote: > biocValid() says all is well ... >

Re: [Bioc-devel] Update of data packages in RTCGA Family/Factory of R Packages

Hi Marcin, I can help you add these to ExperimentHub after the release. There are a few other things I need to tidy so timing will be about mid-May. Note that the new data format should not be data.frames but instead follow what we discussed here: https://tracker.bioconductor.org/issue1335

Re: [Bioc-devel] updated BridgeDbR package

It looks like you're one of the authors but not the maintainer. If you have svn credentials we can give you write permissions to the repo. If you don't have credentials we can request them for you. If you want the changes in quickly you could ask the maintainer to push them. Valerie On

Re: [Bioc-devel] Feedback on OrganismDb development

On 04/08/2016 02:34 PM, Obenchain, Valerie wrote: > Hi, > > It sounds like we have agreement on these points: > > - Add support for sequences > - Keep the OrganismDb name > - Do provide pre-built packages > > I'm not sure we got much weigh in on the package na

[Bioc-devel] Bioconductor 3.3 release: annotation summary

Hi, This is a heads up about a few changes we've made to the production of in-house annotations for Bioconductor 3.3. # Microarray packages: We will propagate but no longer rebuild the ChipDb, probe and cdf packages. These data have been static for some time. The packages will continue to be

Re: [Bioc-devel] Feedback on OrganismDb development

d was wondering what would become of them >> now that Marc moved to Seattle Children's. It is great to hear >> that they will receive renewed attention because it is a really >> handy infrastructure. About all I could ask for is Drosophila, >> Danio, and Caenorhabdit

[Bioc-devel] Feedback on OrganismDb development

BioC developers, After the release we plan to continue development the OrganismDb class and packages. This email outlines some ideas for future direction. We're interested in feedback on these points as well as other thoughts people might have. ## Background The OrganismDb class is defined in

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

> . > Is it a good starting tutorial? > Any tutorial is welcome. > Thanks > Karim > > > > > On Tue, Apr 5, 2016 at 4:11 PM, Obenchain, Valerie > <valerie.obench...@roswellpark.org > <mailto:valerie.obench...@roswellpark.org>> wrote: > > Hi

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

Hi Karim, I can help you put together an annotation package. Here are the general guidelines: http://www.bioconductor.org/developers/package-guidelines/ We ask that annotations packages implement the select() interface from AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can see

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

Thanks for the report. Dan is looking into it. Valerie On 04/04/2016 08:44 AM, Riester, Markus wrote: > Hi, > > my package PureCN started to fail CHECK on Windows (i386 only, x64 seems to > work). > > http://bioconductor.org/spb_reports/PureCN_0.99.6_buildreport_20160402193854.html > > Looks

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

espaceExport > issue somehow, so apologies for wasting your time. > We'll get that cleared and do a new commit. > Thanks > Glyn > > > -----Original Message- > From: Obenchain, Valerie [mailto:valerie.obench...@roswellpark.org] > Sent: 16 March 2016 13:46 > To: Glyn B

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

Hi Glyn, On 03/16/2016 03:20 AM, Glyn Bradley wrote: > Hi All, > > Our package, CausalR, broke when igraph was updated last year. We have now > fixed this, but are having problems uploading the > new version. The package had become depreciated in devel, but there's still a > landing page in

Re: [Bioc-devel] ExperimentHub and existing data in AnnotationHub

Hi Laurent, ExperimentHub won't be in the next release but will be active in the next devel (Bioconductor 3.5). If you want to move your data from AnnotationHub to ExperimentHub I can help with that but not until after the release. We don't have a formal policy but it seems reasonable for the

Re: [Bioc-devel] SVN Commit - Problem with the Version Number

Hi Sandro, The devel and release repositories are distinct. RELEASE: svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/VegaMC DEVEL: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VegaMC Work on the two should be kept separate, ie, to work on

Re: [Bioc-devel] Updating CausalR package after igraph fix

Hi Glyn, It looks like CausalR is broken in release and devel. You'll need to make the changes to both branches - check out, make changes, bump the version and check in. Complete instructions are here: http://bioconductor.org/developers/how-to/source-control/ New functions should be added to

[Bioc-devel] Bioconductor Newsletter: January 2016

http://www.bioconductor.org/help/newsletters/2016_January/ Happy New Year! Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

Thanks! Valerie On 12/17/2015 08:32 AM, Brad Friedman wrote: > Thanks, I've made the corresponding change to release version, and > bumped minor version there. > > I previously only made it to devel. > > Brad > > On Thu, Dec 17, 2015 at 8:21 AM, Obenchain, V

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

Hi Brad, Following up on this because AnalysisPageServer is still broken in release. Can you please fix? Thanks. Valerie On 12/14/2015 01:36 PM, Morgan, Martin wrote: > At least for the R package side of things, I think the question of how to > invoke R CMD in a Makefile is moot for

Re: [Bioc-devel] error in stable AnnotationHub

Hi Kasper, This has been fixed. With the most current AnnotationHub (2.3.3 devel, 2.2.2 release) you should see a snapshot date of 2015-11-05. > hub = AnnotationHub() snapshotDate(): 2015-11-05 > hub[["AH28868"]] require(“rtracklayer”) loading from cache ‘/home/vobencha/.AnnotationHub/34308’

[Bioc-devel] Bioconductor Newsletter - October 2015

Now available at http://www.bioconductor.org/help/newsletters/2015_October/ This issue covers the Bioconductor Core team move, new forums for R/Bioconductor workflows, new functions in the infrastructure and contributed packages, and a few coding insights from Herve. Valerie This email

[Bioc-devel] new Bioconductor team members

In September the Bioconductor project relocated from Seattle, Washington to Buffalo, New York and along with the geographical change came a few staff changes. A big thank you to Marc, Sonail and Paul for their contributions to the project. They were instrumental in the design and implementation

Re: [Bioc-devel] timeout on perceval server macos snow leopard

Hi, I've taken a quick look at LowMACA. It looks like you're doing more work than you need to with 'applyfun'. BiocParallel automatically detects the OS and will use SnowParam, MulticoreParam or SerialParam as needed. The more important problem is that you have several nested layers of parallel

Re: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

Hi Robert, Thanks for reporting the bug. The problem was with how 'X' was split before dispatching to bplapply() and affected both SerialParam and SnowParam. Now fixed in release (1.2.21) and devel (1.3.52). Valerie > > - Forwarded Message - > From: "Robert Castelo"

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