Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote: Here you go ... sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.U

[Bioc-devel] New package for copy number detection from targeted sequencing using off-target reads

I am happy to announce that our CopywriteR tool is now available on the development branch of Bioconductor. CopywriteR extracts copy number information from targeted sequencing using off-target reads (for more information, see Kuilman et al, Genome Biology 16:49, 2015). This new method allows co

[Bioc-devel] AnnotationHub: Error in Docker release_core

Hi, I just started to toy around with the new BioC dockers out of curiosity. As I pulled down the release_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed > library(AnnotationHub) > hub <- AnnotationHub() I received the following

Re: [Bioc-devel] AnnotationHub: Error in Docker release_core

Hi, On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger wrote: > Error in file(con, "r") : cannot open the connection > In addition: Warning message: > In file(con, "r") : unable to resolve 'annotationhub.bioconductor.org' That's strange, on linux it's working. Seems related to network unavaila

[Bioc-devel] Fwd: Proposed biocViews for Hi-C assay

From Aaron Lun. On a related note, there's now a number of packages involved in analyzing Hi-C data, e.g., GoTHiC, HiTC, GenomicInteractions and diffHic. Would it be worth adding a BiocViews term for the Hi-C assay (maybe under Technology -> Sequencing)? Cheers, Aaron -- Aaron Lun PhD student

Re: [Bioc-devel] AnnotationHub: Error in Docker release_core

Dear Elena, thank you for your quick response. Seems as I have make this up to early - it works now for me as well, must have been a pure connection issue. Thx for pointing me to the docker scripts (I must have overread it, is ac tually also stated under http://bioconductor.org/help/docker/). So

Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

Here you go ... > sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en

[Bioc-devel] Announcing a new package: FlowRepositoryR

Hello to those working with flow cytometry data, we are excited to announce that our package, FlowRepositoryR, is now available in BioConductor (devel). This package provides a light interface to access FlowRepository (https://flowrepository.org/) data from within R. FlowRepository is a public repo

[Bioc-devel] Disabling commits to release today; Update NEWS files, biocViews

Hi, Just a reminder that according to the release schedule (http://bioconductor.org/developers/release-schedule/#april-9) we will be disabling commits to the current release (3.0) branch today at 4:20PM Seattle time and then running one last build for that branch. Also, another reminder to pl

[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed > library(AnnotationHub) > hub <- AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter

Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported. On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote: > Hi, > > As I pulled down the devel_core image (running boot2docker under OS X > Yose