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

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

Hello, As an additional wrinkle to this problem, I think that the builds for chipenrich are still using chipenrich.data v1.11.6 instead of the successful chipenrich.data v1.99.10. When I look at the R CMD check errors, I strongly suspect it's because the wrong version of chipenrich.data is

Re: [Bioc-devel] Fwd: Gostats and custom list

Sorry and thanks for the information. On 11 Apr 2017 6:00 p.m., "James W. MacDonald" wrote: > This list is intended for discussions about package development, not > general queries. Please post that sort of question on the support site, > https://support.bioconductor.org > > On

Re: [Bioc-devel] Fwd: Gostats and custom list

This list is intended for discussions about package development, not general queries. Please post that sort of question on the support site, https://support.bioconductor.org On Tue, Apr 11, 2017 at 8:32 AM, amit kumar subudhi wrote: > Hi, > > I am using Gostats to perform

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

Hello, I updated the devel version of chipenrich.data (an experiment package) and got a successful build for v1.99.10 (http://bioconductor.org/checkResults/3.5/data-experiment-LATEST/chipenrich.data/ ), but the

[Bioc-devel] Fwd: Gostats and custom list

Hi, I am using Gostats to perform GO enrichment from custom list of genes and custom annotations. My annotation file looks like this head (geneGO) GOterm evi GeneID 1 GO:0016020 ND PCHAS_010020 2 GO:0016021 ND PCHAS_010020 3 GO:0016020 ND PCHAS_010030 4 GO:0016021 ND PCHAS_010030

Re: [Bioc-devel] Installing EBImage with custom packages dir?

You can always use biocLite(pkg , lib="path/to/library") . The lib path in biocLite defaults to the .libPaths()[1]. When you do .libPaths() upon opening R does your path appear that you set with the environment variables? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute

Re: [Bioc-devel] Installing EBImage with custom packages dir?

Hi, Thanks for your answer. The R_LIBS and R_LIBS_USER environment variables are already set in my ~/.Renviron . They point to the correct location. But this latter is not selected when installing packages with biocLite()... Cheers GM -- Guillaume MULLER, PhD PRESANS - Remix Coworking -

Re: [Bioc-devel] Installing EBImage with custom packages dir?

If you are able to set environment variables or have a .bash_aliases, you could set the R_LIBS or R_LIBS_USER environment variables to your desired path "~/.R/x86_64-pc-linux-gnu-library/3.1.2". When these are set it should become the default path in .libPaths() when you start R. Lori

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

On 04/11/2017 05:01 AM, Gordon K Smyth wrote: The problem appears to be with installed.packages(). If I start a fresh R 3.4.0beta session, then I can run installed.packages() once with correct results, but running it a second time gives the error message: installed.packages() Error in if

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

The problem appears to be with installed.packages(). If I start a fresh R 3.4.0beta session, then I can run installed.packages() once with correct results, but running it a second time gives the error message: > installed.packages() Error in if (file.exists(dest) && file.mtime(dest) >

[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an error message as shown below. What have I overlooked? Thanks Gordon > sessionInfo() R version 3.4.0 beta (2017-04-08 r72499) Platform:

[Bioc-devel] test coverage of a shiny app

Hi I am the developer of the packages Prostar ad DAPAR and I would like to write some unit test for Prostar which contains a Shiny application. I wrote a test script in the 'test' directory where I am using functions from the shiytest package but I don't know how to really test my app