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

ks 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 keeping an eye on the build report. > > Valerie > > > On 06/19/2

Re: [Bioc-devel] Stackoverflow Bounty: pkgdown R package build_site function causes dependent packages unable to be loaded

l advice for any bug report. I don't know if you found > a bug but it could be (hard to tell without being able to reproduce). > > Also did you try to contact the pkgdown folks? This is probably a more > efficient way to report a bug than using stackoverflow. > > Cheers, > H. &

[Bioc-devel] Stackoverflow Bounty: pkgdown R package build_site function causes dependent packages unable to be loaded

I am trying to build a pkgdown documentation for Bioconductor package. I have wrote about it on the stackoverflow http://stackoverflow.com/questions/36874972/pkgdown-r-package-build-site-function-causes-dependent-packages-unable-to-be-loa but the question didn't receivew the expected attention. I

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

; Let me know if you run into problems. > > Valerie > > On 12/01/2016 07:13 AM, Marcin Kosiński wrote: > > Hi Valerie, > > > > Thanks for the responce. Yes I have ExperimentHub in Depends. > > > > In the following code results I present the `query` NOTE that

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

take care of all the warnings you mentioned. > > Are you depending on ExpermentHub? > > Valerie > > On 11/30/2016 09:52 AM, Marcin Kosiński wrote: > > Hi bioc devs! > > > > In this manual about creeating ExperimentHubData package > > http://www.biocondu

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

Hi bioc devs! In this manual about creeating ExperimentHubData package http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html there is a suggestion to create a zzz.R file where `query` function is used. This function comes from AnnotationHub

Re: [Bioc-devel] What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

Marcin Kosiński <m.p.kosin...@gmail.com>: > Dear Bioc devs, > > I am looking for a tool to jointly analyze methylation and expression data > from TCGA. > > As I haven't earlier used R for finding differentially methylated bases or > regions I thought Bioc Views wou

[Bioc-devel] What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

Dear Bioc devs, I am looking for a tool to jointly analyze methylation and expression data from TCGA. As I haven't earlier used R for finding differentially methylated bases or regions I thought Bioc Views would be a great start to look for the tool to analyze the methylation data. I am

[Bioc-devel] BioC 2016 Conference Overview and Few Ways of Downloading TCGA Data

Few weeks ago I have a great pleasure of attending BioC 2016: Where Software and Biology Connect Conference at Stanford, where I have learned a lot! It wouldn’t be possible without the scholarship that I received from Bioconductor

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

Hello bioc developers, Do you maybe know what is the cause of this error? http://bioconductor.org/checkResults/release/bioc-LATEST/RTCGA/moscato2-checksrc.html This is the only platform that has such an error. It appeared frequently recently in RTCGA. Cheers, Marcin [[alternative HTML

[Bioc-devel] [Announcement] RTCGA - Factory of R Packages is Released

Hi all bioc-developers, I have just finished work with RTCGA package and released, on Bioconductor, the *RTCGA Factory of R Packages*. Read this quick guide to find out more about this R Toolkit for

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

2016-05-04 17:22 GMT+02:00 Dan Tenenbaum <dtene...@fredhutch.org>: > That's correct. > Dan > > > - Original Message - > > From: "Andrzej Oleś" <andrzej.o...@gmail.com> > > To: "Robert M. Flight" <rfligh...@gmail.com> > >

[Bioc-devel] downloads number status shields for packages

Hi all, Have anyone considered creating shields (http://shields.io/) with the status of total downloads number for packages held on bioc? This already works for CRAN packages http://cranlogs.r-pkg.org/ It could take total `Nb of downloads` from the right table like here

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

Thanks a lot! So I'll contact you after mid-May :) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

of new resources, immediately after our next release, May 4, so the timing is fairly good.* Does it mean I should upload these data packages before May 4th or after? 2016-04-18 20:04 GMT+02:00 Marcin Kosiński <m.p.kosin...@gmail.com>: > > > 2016-04-16 22:55 GMT+02:00 Martin Mor

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

2016-04-16 22:55 GMT+02:00 Martin Morgan <martin.mor...@roswellpark.org>: > > > On 04/16/2016 01:09 PM, Marcin Kosiński wrote: > >> Hello, >> >> I would like to ask you all for an advice in the following issue. >> >> Last year I have starte

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

Hello, I would like to ask you all for an advice in the following issue. Last year I have started working with data from The Cancer Genome Atlas. During that work out team (https://github.com/orgs/RTCGA/people) have prepared some tools for downloading and integrating datasets from TCGA study and

Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

cess to the same data is beneficial. One possibility is to >> collaboratively curate the data into AnnotationHub / ExperimentHub >> resources, and to tailor access via packages that reference the resource >> (e.g., one can retrieve the GRASP2 data base through AnnotationHub as >> resourc

[Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

I have published `RTCGA.rnaseq` R package that provides datasets from TCGA project containig RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like `RTCGA.RNAseq` and if that's possible, how should I do that and to whom should I