Re: [Bioc-devel] DataFrame conversion

2024-03-13 Thread Ramos Perez, Marcel via Bioc-devel
Hi Daniel, Thanks for posting. Hervé has asked on the R-devel mailing list: https://stat.ethz.ch/pipermail/r-devel/2024-March/083265.html I don't think you will have to do anything in your package. Once fixed, the messages will go away. Best regards, Marcel On 3/13/24 5:09 PM, Daniel

[Bioc-devel] DataFrame conversion

2024-03-13 Thread Daniel Schulz
Dear all, I am maintaining the imcRtools package. Since Monday we have a build error on the development version. Most of the errors are attributed to test functions which fail now and can be attributed to the below problem. It seems that currently with R 4.4 and Bioconductor 3.19 the following

Re: [Bioc-devel] Failed to activate account for Bioconductor git credentials

2024-03-13 Thread Małgorzata Oleś
Dear Lori, the issue described by Ning seems to be the same as I am experiencing right now (new machine + public key in github updated + Bioconductor Git Credentials not recognising my email + g...@git.bioconductor.org: Permission denied (publickey)). Could you assist me here, please? Best

[Rd] R Dev Day @ Imperial, London, Fri Apr 26

2024-03-13 Thread Heather Turner
Dear All, R Dev Day @ Imperial will take place on Friday 26 April at Imperial College London: https://pretix.eu/r-contributors/r-dev-day-imperial-2024/ This event is aimed at current or aspiring R contributors based in the UK. Unlike other contributor events, we may not have representation

[Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"

2024-03-13 Thread Rainer Johannes
Dear all, we're having some rather strange errors with R CMD check on the xcms package recently: it will fail with this warning (which then becomes an error): ✔ checking whether the namespace can be loaded with stated dependencies (5.9s) ✔ checking whether the namespace can be unloaded

Re: [Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

2024-03-13 Thread Matteo Tiberti via Bioc-devel
Hi, I can confirm it did clean up – thanks for your help! Cheers Matteo Tiberti Danish Cancer Institute Strandboulevarden 49 DK-2100 Copenhagen Telephone: +45 35 25 73 07 – a part of the Danish Cancer Society [An image showing the Danish Cancer Society's name and logo called the bow in red

Re: [Rd] Spurious warning in as.data.frame.factor()

2024-03-13 Thread Ivan Krylov via R-devel
В Tue, 12 Mar 2024 12:33:17 -0700 Hervé Pagès пишет: > The acrobatics that as.data.frame.factor() is going thru in order to > recognize a direct call don't play nice if as.data.frame() is an S4 > generic: > >     df <- as.data.frame(factor(11:12)) > >    

Re: [R-pkg-devel] confusion over spellchecking

2024-03-13 Thread Ivan Krylov via R-package-devel
В Sun, 10 Mar 2024 13:55:43 -0400 Ben Bolker пишет: > I am working on a package and can't seem to get rid of a NOTE about > > Possibly misspelled words in DESCRIPTION: >glmmTMB (10:88) >lme (10:82) > > on win-builder. Do you have these words anywhere else in the package (e.g. in the

Re: [R-pkg-devel] Submission after archived version

2024-03-13 Thread Ivan Krylov via R-package-devel
В Mon, 11 Mar 2024 23:45:13 +0100 Nils Mechtel пишет: > Despite R CMD check not giving any errors or warnings, the package > doesn’t pass the pre-tests: If your question was more about the reasons for the difference between your R CMD check and the pre-tests, most of it is due to --as-cran: