Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

Thanks very much! From: Nitesh Sent: 30 November 2016 16:39:34 To: Rodriguez Martinez, Andrea; Kasper Daniel Hansen Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac This

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

This is all I get: > source("https://bioconductor.org/biocLite.R;) Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help > biocLite("MWASTools") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development (unstable) (2016-10-26 r71594).

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

You are not set up to compile from source. Specifically, you're missing a fortran compiler (gfortran) On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea < andrea.rodriguez-martine...@imperial.ac.uk> wrote: > This is all I get: > > > source("https://bioconductor.org/biocLite.R;) >

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

Thanks very much for the clarification. Best wishes, Andrea From: Kasper Daniel Hansen Sent: 30 November 2016 16:26:10 To: Rodriguez Martinez, Andrea Cc: Vincent Carey; bioc-devel@r-project.org Subject: Re: [Bioc-devel] problems

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

This should help: https://cran.r-project.org/bin/macosx/tools/ On Wed, 30 Nov 2016 at 11:29 Rodriguez Martinez, Andrea < andrea.rodriguez-martine...@imperial.ac.uk> wrote: > Thanks very much for the clarification. > > Best wishes, > > Andrea > > > From: Kasper

[Bioc-devel] Error processing scater vignette Mac OS X Sierra

Hi all Since updating to Mac OS X Sierra (the only system change I can think of), building the vignette in scater throws an error. It seems to be caused by excess arguments to pandoc, but this has never been a problem until now (the vignette hasn't changed in any major way for months).

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] Error processing scater vignette Mac OS X Sierra

Hi Davis, Update your BiocStyle package to 2.2.1 (release) or 2.3.12 (devel) which I see you are using at https://github.com/Bioconductor-mirror/scater/blob/master/DESCRIPTION#L24. See https://stat.ethz.ch/pipermail/bioc-devel/2016-November/010168.html for details Best, Leo On Wed, Nov 30, 2016

[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] problems installing cran dependencies with BioC devel in mac

> On Nov 30, 2016, at 4:13 PM, Martin Morgan > wrote: > > On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote: >> Full transcript please; you're compiling from source. > > Excuse my ignorance about the Mac world but shouldn't these be available for > binary

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote: Full transcript please; you're compiling from source. Excuse my ignorance about the Mac world but shouldn't these be available for binary installation via the URL Andrea provided,

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

- Original Message - > From: "Sean Davis" > To: "Martin Morgan" > Cc: "bioc-devel" > Sent: Wednesday, November 30, 2016 1:20:58 PM > Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC

[Bioc-devel] problems installing cran dependencies with BioC devel in mac

Hi, I'm trying to install my MWASTools package (devel branch) in mac, and I get a lot of errors regarding the installation of the dependencies from CRAN because there are no files in the repository: https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/ For windows, I dont have any

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

sessionInfo()? I just did biocLite("MWASTools") with a devel version of R/BiocInstaller, and it seems to work well. On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea < andrea.rodriguez-martine...@imperial.ac.uk> wrote: > Hi, > > > I'm trying to install my MWASTools package (devel