Re: [Bioc-devel] Bioconductor 3.4 is released

On 10/18/2016 06:07 PM, Lorena Pantano wrote: Hi all, I just checked my package and I see some issues, maybe something i did wrong : 1- http://bioconductor.org/packages/release/bioc/html/isomiRs.html : it says this is the

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

Agh, I could have looked better in the Git mirror code ;) Anyway, thanks a lot for the tip! No worries about removing the file if the parent package gets supported. However, I've never tried to run the VEP script on Windows, which I expect is pre-requisite for the package building

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

- Original Message - > From: "Kevin RUE" > To: "bioc-devel" > Sent: Tuesday, October 18, 2016 3:28:23 PM > Subject: [Bioc-devel] Package "not supported" on some platforms, and > dependent packages > Hi all, > > Heartless logic

Re: [Bioc-devel] staging.bioconductor.org not responsive

Sorry, bioc-devel, that email wasn't meant for you! Martin On 10/18/2016 06:25 PM, Martin Morgan wrote: Hi Dan, et al., When I try to ssh I get $ ssh ubu...@staging.bioconductor.org ssh_exchange_identification: read: Connection reset by peer and it seems like the sync with master didn't

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

Hi all, Heartless logic works as follows: - ensemblVEP is "not supported" on Windows (build report ). Completely understandable. - My package depends on ensemblVEP. - The build system reports an error on Windows

Re: [Bioc-devel] staging.bioconductor.org not responsive

Try ssh'ing as the biocadmin user, not ubuntu. I am able to do both but that just might mean my public keys are in both places. There is a crash.log in /home/biocadmin/bioc-test-web/bioconductor.org which may have some hints as to what happened. Dan - Original Message - > From:

[Bioc-devel] staging.bioconductor.org not responsive

Hi Dan, et al., When I try to ssh I get $ ssh ubu...@staging.bioconductor.org ssh_exchange_identification: read: Connection reset by peer and it seems like the sync with master didn't happen at 3pm / 3:20pm. Hints? If there was a commit problem, it's most likely config.yaml at

Re: [Bioc-devel] Bioconductor 3.4 is released

Hi all, I just checked my package and I see some issues, maybe something i did wrong : 1- http://bioconductor.org/packages/release/bioc/html/isomiRs.html : it says this is the development page, I guessed that this will go, but

[Bioc-devel] Bioconductor 3.4 is released

Thanks to all the developers for your contribution to the project! --- --- October 18, 2016 Bioconductors: We are pleased to announce Bioconductor 3.4, consisting of

[Bioc-devel] Ascona Workshop 2017: Call for abstracts

Ascona Workshop 2017 -- Statistical Challenges in Single-Cell Biology Abstract Submission now open! We would like to announce and invite your participation in a workshop on Statistical Challenges in Single-Cell Biology, to be held from April 30 to May 5, 2017, at Monte Verità, Ascona, in the

Re: [Rd] Cluster: Various GCC, how important is consistency?

Dear Jeroen Did you rebuild R-3.3.1 and all of the packages with GCC-5.3 in order to make this work? The part that worries me is that the shared libraries won't be consistent, with various versions of GCC in play. On Tue, Oct 18, 2016 at 5:55 AM, Jeroen Ooms wrote:

Re: [Rd] weird dir() behavior with broken symlinks

another strange behavior of list.dirs(), that seems related: docker run -ti rocker/r-base > setwd(tempdir()) > file.symlink('from', 'to') [1] TRUE > list.dirs(recursive=FALSE) [1] "./to" > file.symlink('C/non_existing.doc', 'broken.txt') [1] TRUE > list.dirs(recursive=FALSE) [1] "./broken.txt"

[Rd] weird dir() behavior with broken symlinks

I encountered very weird behavior of the dir() function, that I just can not understand. Reproducible example: docker run -ti rocker/r-base R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > #

Re: [Rd] Cluster: Various GCC, how important is consistency?

On Tue, Oct 18, 2016 at 1:44 AM, Paul Johnson wrote: > > Administrator suggested I try to build with the GCC that is provided > with the nodes, which is gcc-4.4.7. Redhat provides an alternative compiler (gcc 5.3 based) in one of it's opt-in repositories called "redhat

Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

Thanks Hervé. R. On Mon, 17-10-2016, at 11:32, Hervé Pagès wrote: > Hi Ramon, > > Yes the issue is known. The vsn maintainers have fixed the problem > yesterday in svn, right before the builds started. All the failures > due to vsn not installing on the build machines