Re: [Bioc-devel] Question with push to remote repository

2021-03-22 Thread Nitesh Turaga
Hi Lauren, Maybe the right key wasn’t added, you need to figure it out with Tim if you continue with this approach. Please check if the key added was correct on BiocCredentials, and on your end, please check if you are using the right key-pair. Best, Nitesh From: "Harmon, Lauren" Date:

Re: [Bioc-devel] EXTERNAL: Resolve mismatch between master and release branches

2021-03-22 Thread Marcel Ramos
Hi Sarah, The release branch is meant for bug fixes that ensure the stability of the code. It does not usually include 'updates' from the devel. The way to cleanly do this is to hard reset to a previous commit. The commit where your packages version was bumped for the 3.12 release. You can

[Bioc-devel] Resolve mismatch between master and release branches

2021-03-22 Thread Sarah Voisin
Hi, I have updated the master branch of my MEAT package yesterday ( https://github.com/sarah-voisin/MEAT), and I tried updating the release branch as well (RELEASE_3_12), but I must have messed up since the release branch is now 7 commits behind master and 3 commits ahead, and I am stuck. How do

[Bioc-devel] May 3 – May 14, 2021, online: May Institute on computation and statistics for mass spectrometry and proteomics

2021-03-22 Thread Dan Guo
Dear Colleagues: May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on May 3 � May 14, 2021 on the Boston campus of Northeastern University (online), is now accepting applications. The program includes tutorials and practical hands-on sessions,

Re: [Bioc-devel] Question with push to remote repository

2021-03-22 Thread Nitesh Turaga
Hi, It's possible you aren't using the correct SSH key? Why does it show t.triche as the key user? Best, Nitesh On 3/22/21, 2:28 PM, "Bioc-devel on behalf of Harmon, Lauren" wrote: Hello, I have a quick question! I accidentally committed a large file to a bioconductor

[Bioc-devel] Question with push to remote repository

2021-03-22 Thread Harmon, Lauren
Hello, I have a quick question! I accidentally committed a large file to a bioconductor repository, and I am trying to remove it from the history with bfg. That works fine, but when I try to push my changes, I get this error: lauren.harmon@C02CG5WTLVDL spiky.git % git push Enter passphrase

Re: [Bioc-devel] Methods to speed up R CMD Check

2021-03-22 Thread Hervé Pagès
Hi Alan, It looks like what is slowing everything down significantly is the approach you've taken to look up the ExperimentHub resources that you control by name every time you need to access them. E.g: Look up by name: > system.time(tt_alzh <- ewceData::tt_alzh()) snapshotDate():

Re: [Bioc-devel] Methods to speed up R CMD Check

2021-03-22 Thread Martin Morgan
if your examples repeatedly calculate the same thing, and this is also typical of how users use your package, it might make sense to 'memoise' key functions in your package https://cran.r-project.org/package=memoise Martin On 3/22/21, 7:41 AM, "Bioc-devel on behalf of Kern, Lori" wrote:

Re: [Bioc-devel] Bioconductor Git Credentials error

2021-03-22 Thread Nitesh Turaga
Hi, You cannot have two maintainers to a package. We operate under the assumption that there is a single maintainer per package. The user that has access to the package is �j.chen2�., there are no SSH keys with that username so there is no access. I�ve deleted the other account with username

Re: [Bioc-devel] Methods to speed up R CMD Check

2021-03-22 Thread Kern, Lori
If your data is using ExperimentHub, it should already be caching the downloaded data. Once it is downloaded once, it should be using the cached download for subsequent calls to the hub. We will investigate to ensure that the caching mechanism is functioning properly on all of our

Re: [Bioc-devel] Bioconductor Git Credentials error

2021-03-22 Thread raman sethi
Hi Nitesh, Our account is activated already. Thank you Best Regards Raman On Sat, Mar 20, 2021 at 10:31 PM Nitesh Turaga wrote: > Did you activate your account first? > > > > > > > > *From: *raman sethi > *Date: *Friday, March 19, 2021 at 10:33 PM > *To: *Nitesh Turaga > *Cc: *Bioc-devel

[Bioc-devel] Methods to speed up R CMD Check

2021-03-22 Thread Murphy, Alan E
Hi all, I am working on the development of [EWCE](https://github.com/NathanSkene/EWCE) but have hit an issue with R CMD check's runtime. I have been informed this test needs to be completed in 15 minutes but mine is currently running in ~24 minutes and I am looking for methods to speed this