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’

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

[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] 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"

[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

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] 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] 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

[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] 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

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] 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] 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] 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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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

[Bioc-devel] tokay2 outage

Hi, We've been having problems with our Windows devel builder, tokay2 (https://stat.ethz.ch/pipermail/bioc-devel/2017-January/010424.html). It's been determined the battery for the storage array is bad and needs to be replaced. The work is scheduled for tomorrow, Thursday Feb 2 at at 10am EST.

Re: [Bioc-devel] biocViews and experiment data

http://www.bioconductor.org/packages/3.5/data/experiment/VIEWS Val On 02/02/2017 08:20 AM, Laurent Gatto wrote: > Dear all, > > What is the equivalent of this URL > > http://www.bioconductor.org/packages/3.5/bioc/VIEWS > > for data/experiment packages? > > Thank you in advance. > > Laurent >

Re: [Bioc-devel] tokay2 outage

The battery has been replaced and tokay2 appears to be functioning normally. Today's builds (Feb 2) won't include tokay2 because it hung again yesterday but starting tomorrow we should be back on track. Valerie On 02/01/2017 08:30 AM, Obenchain, Valerie wrote: > Hi, > > We've be

Re: [Bioc-devel] xps build problem on toluca2

esponsible for the setup. If this is > the case I will in the future contact you. > > Best regards, > Christian > > > On 01/27/17 15:46, Obenchain, Valerie wrote: >> Hi Christian, >> >> toluca2 is in the process of being set up and oaxaca is still the >> off

[Bioc-devel] tokay2: devel Windows builder

Hi, Just a heads up that we're having intermittent problems with the Windows devel builder, tokay2, located on site at RPCI. About a week ago, RPCI had a problem with back-up power that has since been resolved. Because we continue to see problems with tokay2 (but none of the other servers) it's

Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error

Thanks for the report. It looks like the directory structure has changed. I'll work on this tomorrow and will post back when it's fixed. Valerie On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: > Hello, > > I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): > >>>

Re: [Bioc-devel] xps build problem on toluca2

Hi Christian, toluca2 is in the process of being set up and oaxaca is still the official Mac devel builder. There are a number of dependencies that need to be addressed on the new machine and we are working through them. It is important to understand that the error on toluca2 does not affect you

Re: [Bioc-devel] LOBSTAHS dev build failing on toluca2; version does not update in devel

Hi, Just to clarify, we do have daily software builds that start at 2:15pm PST. We did not have a devel build report this week on Tuesday, Jan 24 due to a problem with the postrun script. AFAIK that is the only day this week we haven't had a full build report. Looking at the svn logs for

Re: [Bioc-devel] LOBSTAHS dev build failing on toluca2; version does not update in devel

This should have said 2:15pm PST deadline, not 2:25pm. > Looking at the svn logs for LOBSTAHS in devel, there were quite a few > commits on Jan 25. About 1/3 were before the 2:25pm deadline. These were > probably the commits that straddled the deadline: This email message may contain legally

[Bioc-devel] Mac devel builds: oaxaca update

Hi, oaxaca has been in and out of the build report the past couple of days because it was not completing on time. The machine has been rebooted and should be back in today's report (Feb 23). Transitioning to toluca2 as the primary Mac devel builder is a priority for us over the next couple of

Re: [Bioc-devel] update R devel on builders

it's on schedule for today and should be in the Feb 17 report. Valerie On 02/14/2017 05:05 PM, Obenchain, Valerie wrote: > Hi, > > Today we updated R devel on malbec2 and tokay2. Tomorrow we'll work on > oaxaca and toluca2. There may be some unexpected failures on the Single >

Re: [Bioc-devel] makeTxDbPackage bugs in Bioconductor 3.5

Hi Keith, On 02/08/2017 11:37 AM, Keith Hughitt wrote: > Greetings, > > I came across a couple issues when working with the most recent version of > GenomicFeatures (Bioconductor 3.5/Github). > > 1) The "Resource URL" metadata field is only set via some of the helper > functions (e.g.

Re: [Bioc-devel] ERROR: dependency ‘RMySQL’ is not available for package ‘anamiR’

Hi Ti-Tai, The mac binaries for CRAN packages aren't available for R devel yet ... and at this point may not be until the next release in April. On the landing page you can see the only mac binaries are for R release: https://cran.r-project.org/web/packages/RMySQL/index.html Thanks for keeping

Re: [Bioc-devel] Code quality and bug reports

parts of the package review process that could be improved such as requiring unit tests instead of suggesting them. But again, having unit tests does not guarantee that all (or the most important) aspects of the package are tested. Valerie > Thanks, > > Lluís > > On 6 January 2017 at 18:56,

[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] 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

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] 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] 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

[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

[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

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

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] 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] Coverage test badge not updating

(matching https://codecov.io/github/Bioconductor-mirror/recount?branch=master > ) > > It could be related to recount failing the latest build report on > release. Or maybe it's another alphabetical bug because the derfinder* > packages look ok. > > Best, > Leo > > On

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] Coverage test badge not updating

Coverage is now up and running for the release packages. I think all looks well... let me know if you see any problems. Valerie On 11/01/2016 03:14 PM, Hervé Pagès wrote: > Hi Leo, > > I can confirm that while Bioc 3.4 was in devel, package coverage was > computed only for the devel version of

Re: [Bioc-devel] moving package from annotation to experiment data

Can you give me some background? Was this recently added or did it get added to the wrong repo? Val On 12/09/2016 07:42 AM, Kasper Daniel Hansen wrote: > The package > FlowSorted.CordBloodNorway.450k > should be moved from Annotation to ExperimentData. Not sure how to do this. > > Best, >

Re: [Bioc-devel] Query about hgu133plus2 database

This question is more appropriate for the support site. Please ask there and show the output of your sessionInfo(). https://support.bioconductor.org/ Valerie On 12/05/2016 01:15 PM, Bhattacharya, A (onco) wrote: > Hi, > > I was trying to get the gene mapping for one of the datasets in

Re: [Bioc-devel] ‘gWidgets2RGtk2’ is not available in malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64

Hi Hemi, Thanks for the report . We're looking into this ... Valerie On 12/11/2016 05:31 PM, Luan Hemi wrote: > Dear sir or madam, > > The gWidgets2RGtk2 seems not to be at malbec1 Linux and causes some > problems. Could anyone give some helps? > >

Re: [Bioc-devel] Reading files with HTqPCR

Hi Nadine, Please post the question on our support site: https://support.bioconductor.org/ Show the code you tried and the error message (vs sending the file). Tag the question with THqPCR and show the output of sessionInfo(). Valerie On 12/13/2016 08:05 AM, Nadine Hoffmann wrote: > Hello

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

ase vignette > https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html > > > 2016-12-05 17:54 GMT+01:00 Obenchain, Valerie > <valerie.obench...@roswellpark.org > <mailto:valerie.obench...@roswellpark.org>>: > >

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

There is a section in the vignette that describes what should be imported: DESCRIPTION / NAMESPACE The package should depend on and fully import ExperimentHub. ... ExperimentHub depends on AnnotationHub. When ExperimentHub is loaded you can see AnnotationHub attached to the search path with

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Hi, We need to make several updates to the mac machines. These are the last 2 builders that still need to move from the Hutch to RPCI. Because they are still at the Hutch, access to them is limited. We will get to these updates as soon as we can. Valerie On 12/05/2016 01:27 PM, Dan Tenenbaum

Re: [Bioc-devel] Code quality and bug reports

On 01/04/2017 07:53 AM, Lluís Revilla wrote: > Dear Guangchuang and all, > > Quality of the packages has been a preoccupation of the project from > the beginning (see > https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for > more references and other discussions about bug reports.)

Re: [Bioc-devel] report package issue to Bioconductor

Hi, It looks like CorMut doesn't have a github repo so the best approach is to contact the maintainer directly or cc them (zpl...@gmail.com) instead of creating your own gist. Maybe you've tried this? Once the transition from svn to git / github is complete you can open issues or submit a pull

Re: [Bioc-devel] report package issue to Bioconductor

On 01/06/2017 09:53 AM, Obenchain, Valerie wrote: > Hi, > > It looks like CorMut doesn't have a github repo so the best approach is > to contact the maintainer directly or cc them (zpl...@gmail.com) instead > of creating your own gist. Maybe you've tried this? Once the transition

Re: [Bioc-devel] change of maintainer's mail address on release branch

Hi Thomas, Yes, follow the guide lines at the link you cited. ## check out release svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/yourPackage ## make the email change, bump the version and check in cd myPackage svn ci Valerie On 12/20/2016 05:56 AM, Thomas

Re: [Bioc-devel] hg133plus2.db

I think you're missing a 'u', > biocLite("hgu133plus2.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable) (2016-10-22 r71581). Installing package(s) ‘hgu133plus2.db’ trying URL

Re: [Bioc-devel] adding a package maintainer

Hi Stephanie, You can modify the maintainer name/email in the DESCRIPTION file yourself by checking out of svn, make the change and then commit. ## release svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/packageName ## devel svn co

Re: [Bioc-devel] ‘gWidgets2RGtk2’ is not available in malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64

It looks like this has cleared up. We couldn't find anything reproducible so maybe it was a glitch. Valerie On 12/13/2016 07:00 AM, Obenchain, Valerie wrote: > Hi Hemi, > > Thanks for the report . We're looking into this ... > > Valerie > > On 12/11/2016 05:31 PM, Luan He

Re: [Bioc-devel] Bioconductor 3.5 release: deprecated packages

Sorry, xcms was a mistake on my part. This package is not deprecated. Valerie On 03/23/2017 10:06 AM, Obenchain, Valerie wrote: > Just a heads up about deprecated packages. > > These have been 'deprecated' in Biocondcutor 3.4 and will be 'defunct' > in Bioconductor 3.5. The 'def

Re: [Bioc-devel] Rdevel on Windows

I've asked Lori to kick off a new build to see if the windows timeout is reproducible and to get linux results. In general, yes, the full review does not start until the package passes build and check on all platforms. Any further comments I'll post on the github tracker (i.e., not here). Valerie

[Bioc-devel] Annotation packages maintained by Francesco Ferrari

Hi, We have 24 annotation packages in the repo maintained by Francesco Ferrari, the majority of which are broken (output below). The last time these were updated was for Bioconductor 2.8 (3 years ago). We've tried a number of times to contact Francesco but did not get a response. The plan is to

[Bioc-devel] builds: veracruz2 Mac builder

Hi, We recently learned that R 3.4.0, to be released on April 21, will use OS X 10.11 (El Capitan). This means we need a new devel Mac builder up and running before the next release. toluca2 will also become an El Capitan builder but not until after the release. Over the past week, Herve has

Re: [Bioc-devel] builds: veracruz2 Mac builder

Minor correction below: On 03/22/2017 12:56 PM, Obenchain, Valerie wrote: > Hi, > > We recently learned that R 3.4.0, to be released on April 21, will use > OS X 10.11 (El Capitan). This means we need a new devel Mac builder up > and running before the next release. toluca2 w

Re: [Bioc-devel] xps build problem on veracruz2

Hi, veracruz2 is in testing / setup stage and is not the official Mac devel builder. See my post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010629.html Currently there are more pressing issues than the ROOT system dependency. Rest assured that ROOT will be correctly installed

[Bioc-devel] Bioconductor 3.5 release: contributed annotation packages

Dear annotation contributors, Just a reminder the deadline to update annotation packages is Friday April 7. Please make updated packages available via dropbox or another location that allows wget. Indicate if the old version should be included in the upcoming release or if the new package should

Re: [Bioc-devel] Using LaTeX packages in vignettes

Hi, On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote: > Hello all, > > We wrote our vignette in Sweave/LaTeX, and I am running into a problem with > citing to other papers. > I would like to use the APA style of citing which looks like: "Determine the > optimal factorization rank using the NMF

Re: [Bioc-devel] Error in veracruz2: object 'R_svmtrain' not found

Hi, Looks like this was a glitch in rtracklayer and has been fixed: r127902 | m.lawrence | 2017-03-31 04:37:23 -0700 (Fri, 31 Mar 2017) | 2 lines do not try to import pmapFromTranscripts from GenomicAlignments My guess is

[Bioc-devel] Bioconductor 3.5 release

Hi all, The release of Bioconductor 3.5 will be Tuesday, April 25. Please see the schedule for details: http://www.bioconductor.org/developers/release-schedule/ Over the next month we'll announce the key deadlines on bioc-devel. Lori sent the first one last week and it's important for anyone

Re: [Bioc-devel] enable windows build for eiR

Done. I also bumped the version. We missed the cutoff for today so we should see the Windows build on the March 16 report. Valerie On 03/14/2017 03:09 PM, kho...@cs.ucr.edu wrote: > Can you please enable building on windows again for package eiR in > development (current version is 1.15.3)? Not

Re: [Bioc-devel] release schedule

Hi Tyler, Yes, there is another release coming up. We usually release a day or two after R does so we don't set a date until R has announced theirs. As soon as we know the R schedule we'll make an announcement on bioc-devel and the support site. I'll also post the new release schedule. Valerie

Re: [Bioc-devel] tximport fails to build on Windows

Hi Mike, Here is a more informative error from Stangling and sourcing the vignette on the Windows builder: ... reading in files with read_tsv 1 Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file

Re: [Bioc-devel] Devel landing page version not updated after successful build

Hi Raymond, I think this is my fault. I accidentally turned off the cronjob that refreshes/syncs the experiment data repos on the master builder. The job has been reinstated and should run for today's builds. Thanks for catching this and sorry for the inconvenience. Valerie On 04/11/2017 12:25

[Bioc-devel] Bioconductor 3.5 Release: db0 packages

The new db0 packages (all version 3.4.2) are now available in the devel repo. Let me know if you notice any problems. Thanks. 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

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

We've updated the release schedule and moved the deadline for errors to next Friday, April 14. Valerie On 04/06/2017 10:29 AM, Stian Lågstad wrote: > How does the error deadline tomorrow (http://www.bioconductor.org/ > developers/release-schedule/) affect packages that are still red because of

[Bioc-devel] Bioconductor 3.5 release: db0, OrgDb and TxDb packages

Hi, The new db0, OrgDb and TxDb packages are now available in the devel branch. # db0: Updated all 19: anopheles.db0_3.4.2.tar.gz chicken.db0_3.4.2.tar.gz fly.db0_3.4.2.tar.gz pig.db0_3.4.2.tar.gz xenopus.db0_3.4.2.tar.gz arabidopsis.db0_3.4.2.tar.gz chimp.db0_3.4.2.tar.gz

Re: [Bioc-devel] R CMD check error on shinytest package

Hi Sam, Yes, this is a problem. Packages you depend on must be in a CRAN or Bioconductor repository. Valerie On 04/12/2017 10:33 PM, Samuel Wieczorek wrote: > Hi > > For the Prostar package, I began to use the funtionnalities of shinytest > wich is a package that provides utilities to

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

leads to differences in the tests. They all pass on our > machines, so it's hard for us to debug this in a timely manner. > > Thanks! > > Kind regards, > Roel Janssen > > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf

[Bioc-devel] Bioconductor 3.5 release: potential deprecations

Hi, Due to errors / unresponsive maintainers this new group of packages has been identified for potential deprecation in Biocondcutor 3.5. anamiR FunChiP MutationalPatterns seqplots snm ssviz stepwiseCM ToPASeq If anyone is interested in taking over as maintainer please let us know. If not

Re: [Bioc-devel] Error in tokay2

EventPointer 0.99.36 built clean today: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/14/2017 09:16 AM, Obenchain, Valerie wrote: > Hi Juan Pablo, > > We think this is a problem related to installed.packages(), see > discussion here: > > ht

Re: [Bioc-devel] build on different version

Version 1.11.10 posted today: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ For now I would not worry about the error on toluca2. Valerie On 04/14/2017 02:42 AM, Robert Castelo wrote: > hi, > > on tuesday april 11th i checked in changes for VariantFiltering version > 1.11.10

Re: [Bioc-devel] Error in BUILD report (anamiR)

It looks like this has been resolved on today's report: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/07/2017 02:21 PM, 王棣台 wrote: > Hi all, > > I got en error when it tries to create vignette in BUILD: > tokay2 Windows Server 2012 R2 Standard / x64 > > Error:

Re: [Bioc-devel] Error in tokay2

Hi Juan Pablo, We think this is a problem related to installed.packages(), see discussion here: https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010819.html You can ignore this for now. Thanks for keeping an eye on the build report. Valerie On 04/14/2017 12:41 AM, Romero, Juan Pablo

Re: [Bioc-devel] citation on landing page does not update

Looking at the build logs we see this error for the data package: ERROR: extractCitations tarball: /home/biocadmin/PACKAGES/3.5/data/experiment/src/contrib/pathprintGEOData_1.0.0.tar.gz error: /tmp/Rtmpo8k7A4/pathprintGEOData/inst/CITATION:18:181: unexpected symbol 17: pages ="68--81",

Re: [Bioc-devel] How to solve warnings generated by loading other packages

Hi, I'll respond on the github issue tracker where the package review is taking place. Valerie On 04/21/2017 08:27 AM, Kristoffer Vitting-Seerup wrote: > Hi Everybody > > I'm currently in the process of adding my newest R package to Bioconductor > and the last issue I need to solve i a warning

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