Re: [Rd] In base R: argument `list` does not accept lists

On 13/04/2018 7:21 AM, Johannes Rauh wrote: The function `base::rm` has an argument that is named `list`. However, if a list is passed as `list` to `rm` (e.g.: `rm(list = list("x", "y"))`), an error is raised: "invalid first argument". Agreed, the documentation says that `list` should be "a

[Rd] Fwd: suggested patch for messages

Any follow-up/comments on this? If I don't hear back I'll submit to r-bugs so it doesn't get lost ... (Don't see any changes in QC.R in the last few days ... https://github.com/wch/r-source/commits/trunk/src/library/tools/R/QC.R ) -- Forwarded message -- From: Ben Bolker

Re: [Rd] In base R: argument `list` does not accept lists

On Fri, Apr 13, 2018 at 3:51 PM, Duncan Murdoch wrote: > On 13/04/2018 7:21 AM, Johannes Rauh wrote: >> >> The function `base::rm` has an argument that is named `list`. However, if >> a list is passed as `list` to `rm` (e.g.: `rm(list = list("x", "y"))`), an >> error is

[Rd] In base R: argument `list` does not accept lists

The function `base::rm` has an argument that is named `list`. However, if a list is passed as `list` to `rm` (e.g.: `rm(list = list("x", "y"))`), an error is raised: "invalid first argument". Agreed, the documentation says that `list` should be "a character vector naming objects to be

[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

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

Begin forwarded message: From: ni41435_ca > Subject: Re: [Bioc-devel] Bioconductor Git Access: GateFinder Date: April 13, 2018 at 2:43:04 PM EDT To: Tony Culos > Cc: bioc-devel

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

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,

[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

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

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

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

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: > >

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() - >

[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] 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

Re: [Bioc-devel] Need some help to submit a R package.

Dear Sir, I have submitted an R package named "sigFeature" in Github and also Bioconductor 9 days before. The reviewers only said that there is some WARNING problem in the package in different platform. But after that they are not communicating any thing regarding the package. I have checked

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.

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