Re: [Bioc-devel] AAString - Amino acid code enforced?

Hi Felix, Please see my answer in the issue you opened on GitHub: https://github.com/Bioconductor/Biostrings/issues/10 Cheers, H. On 04/02/2018 06:07 AM, Felix Ernst wrote: Dear all, probably this is for Hervé Pagès: I tried the following code, which should according to ?AAString not wor

[Bioc-devel] GateFinder Write Permission

Hey Nima, I have been told I do not actually have write access to GateFinder and need to get your permission to access the package. Thanks, Tony [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.c

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

Hi Tony, Another thing, I checked your Github repo. Please do not push a commit like this to upstream, "test commit: changing name and pushing to test upstream access”. The Bioconductor version of the repo is canonical. You cannot go back in time on that repo. You can test upstream access by u

[Bioc-devel] Fwd: Bioconductor Git Access: GateFinder

Begin forwarded message: From: ni41435_ca mailto:nitesh.tur...@roswellpark.org>> Subject: Re: [Bioc-devel] Bioconductor Git Access: GateFinder Date: April 13, 2018 at 2:43:04 PM EDT To: Tony Culos mailto:tonycu...@gmail.com>> Cc: bioc-devel mailto:bioc-devel@r-project.org>> Hi Tony, You don’t

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

Hi Tony, You don’t have access to that package. I’ve checked the package DESCRIPTION and there is no record of you. Please ask the authors for access to the package. Author: Nima Aghaeepour , Erin F. Simonds Maintainer: Nima Aghaeepour Copy bioc-devel on the email where you ask the authors

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Thank you Andrzej for the info! ## Re-point (1) Regarding my (1), I got my github repo in sync following http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ and http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- It all worked with

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

You are using the HTTPS protocol instead of SSH. Please refer to http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream should look like “g...@git.bioconductor.org:packages/GateFinder.git”. Nitesh > On Apr 13, 2018, at 1:44 PM, Tony Culos wrote: > > Hello, > > I recently

Re: [Bioc-devel] TIMEOUT on package MEAL

It is by fluke that the windows did not time out... The builders timeout occur at 2400 sec and you are right up against the edge at 2145.4 seconds on windows. The build reports include an EllapsedTime indication in the summary section for each builder ... Your package does not meet the requi

[Bioc-devel] Bioconductor Git Access: GateFinder

Hello, I recently received an email from maintai...@bioconductor.org saying that I have access to the GateFinder package however when I try the command "git push upstream master", I receive the error: fatal: remote error: FATAL: W any packages/GateFinder nobody DENIED by fallthru (or you mis-spel

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Hi Michael, Thanks for looking into this. Can you or someone with push permission to S4Vectors implement the workaround that you mentioned? Happy to create a pull request on Github if that helps. We’re trying to solve this to fix the clusterExperiment package build on Bioc-devel. Thanks, Dav

Re: [Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

Generally this means that there are multiple locations where the package is installed - as determined by .libPaths() - The single package builder specifies a package specific place to install packages that are not installed by the daily builder C:/Users/pkgbuild/packagebuilder/workers/jobs/704

[Bioc-devel] Workflow Package Updates / Guidelines

As mentioned before the workflows are in git and are now building on our standard build machines. The build reports are generated mon, wed, fri and can be seen here http://bioconductor.org/checkResults/3.7/workflows-LATEST/ Moving forward we want to align how we treat workflows with how we treat

Re: [Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

Thanks, Lori. The package masking problem went away a few days ago. - Paul > On Apr 13, 2018, at 10:31 AM, Shepherd, Lori > wrote: > > Generally this means that there are multiple locations where the package is > installed - as determined by .libPaths() - > > The single package builder sp

Re: [Bioc-devel] TIMEOUT on package MEAL

Hi BiocDevel, Could you help me with this issue? The report is not very informative. I suspect that the vignettes are taking too long but I have two vignettes and I don't know which one is more problematic. I don't understand either why I have a timeout in OS and Linux but not in Windows. Wh

Re: [Bioc-devel] commit not appearing in report

version 0.99.22 is what is in the git.bioconductor.org repository - It can take up to 24 hours from when you commit to see it reflected on the build report http://bioconductor.org/checkResults/3.7/bioc-LATEST/ Note: This is still yesterday's build report - today's should be up very soon

[Bioc-devel] commit not appearing in report

Dear Community, I have done a commit the 11th of April that does not appear anywhere. My package is ChIPSeqSpike and the last push should be 0.99.22. The build report indicates: *ChIPSeqSpike 0.99.21* Nicolas Descostes Last Commi