[R-pkg-devel] R Package Submission
Dear Sir / Ma'am, Greetings. I am but a newbie in R Package development and currently, I am trying to submit my second package to CRAN and every time after submission, the results for the pre-tests come back 'does not pass the incoming checks automatically'. The NOTE says; Possibly misspelled words in DESCRIPTION: ProteinPCA (9:45, 12:19) ggplot (12:5) The name of the package is ProteinPCA and I have already checked multiple times the Description files for any possible misspellings but I have not found any. Same goes with ggplot2. At this moment, I am really at loss on how to resolve this issue. Could you perhaps enlighten me on this? Thank you very much. Sincerely, *P. A. C. Manlapaz, RCh* [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Warnings and notes while building package with nimble
Hi, I am trying to submit a package to CRAN built using nimble. It generates warnings like so: : no visible global function definition for 'nimDim' and fails automatic checks by CRAN. Any help is appreciated. Thanks and regards, Aritra [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Retrieving versioned csv datasets for use in an R package
Hi, all. Zenodo does offer storage (I believe limited to 50GB per submission) and is backed by CERN with a guarantee of storage for at least 20 years (the life of CERN, could be extended). I agree that Github is a viable alternative to Zenodo and one can use the two together easily. On github, one can use three different approaches: 1) check files into version control, 2) use git lfs, and 3) as release artifacts. Each has pros and cons. If data are of a biomedical nature, one can ofter deposit in a biomedical repository, including one of dozens at NIH and EBI. NIH even recommends some open “generalist repositories” that include zenodo and OSF: https://www.nlm.nih.gov/NIHbmic/generalist_repositories.html If one is looking to cater to the machine learning/AI community, hosting on huggingface is another option. Doing so is quite similar to hosting on github from a purely practical perspective. Cloud storage systems such as AWS, GCP, and Azure are possibilities, but egress charges can be challenging to predict. Cloudflare R2 is s3-compatible and has no egress charges, making it a good choice for sharing particularly large files. On the client side, Bioconductor has BiocFileCache which is a client-side package for caching files that have been downloaded. Other file download/cache packages are available, though I’m less familiar with them. Just wanted to expand the list a bit. Sean From: R-package-devel on behalf of Dirk Eddelbuettel Date: Saturday, February 15, 2025 at 10:29 AM To: Simon Urbanek Cc: R-package-devel@r-project.org Subject: Re: [R-pkg-devel] Retrieving versioned csv datasets for use in an R package On 15 February 2025 at 19:50, Simon Urbanek wrote: | Github is not reliable enough for reproducible research (your files can | disappear at any point - or can change without notice), I'm curious: Do you have a concrete example of a no-longer-reproducible study whose data or other support files changed and thereby caused this breakage? | that's why Zenodo was created. But AFAIK Zenodo offers DOI issuance only, not storage (as, say, OSF would). So this does not address the problem faced by the OP. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R Package Submission
See my response in the communication among you and CRAN. Best, Uwe Ligges On 05.04.2025 08:40, Paul Angelo Manlapaz wrote: Dear Sir / Ma'am, Greetings. I am but a newbie in R Package development and currently, I am trying to submit my second package to CRAN and every time after submission, the results for the pre-tests come back 'does not pass the incoming checks automatically'. The NOTE says; Possibly misspelled words in DESCRIPTION: ProteinPCA (9:45, 12:19) ggplot (12:5) The name of the package is ProteinPCA and I have already checked multiple times the Description files for any possible misspellings but I have not found any. Same goes with ggplot2. At this moment, I am really at loss on how to resolve this issue. Could you perhaps enlighten me on this? Thank you very much. Sincerely, *P. A. C. Manlapaz, RCh* [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and notes while building package with nimble
Hi Aritra, It would be helpful if we can explore the package source code. It helps to provide a more accurate answer. But you will find some other cases on the archive of the mailing list with similar messages. The message indicates that the static code analyzer hasn't detected the definition of the object but detected it is used. This is often the case if you use subset, within or dplyr, ggplot2, data.table or other packages that use delayed evaluation. To solve it, it might be as simple as writing nimDim <- NULL inside your package or there might be a real issue there. Best, Lluís On Sat, 5 Apr 2025 at 18:25, Halder,Aritra wrote: > Hi, > > I am trying to submit a package to CRAN built using nimble. It generates > warnings like so: > > : no visible global function definition for 'nimDim' > > and fails automatic checks by CRAN. Any help is appreciated. > > Thanks and regards, > > Aritra > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and notes while building package with nimble
On 6 April 2025 at 01:25, Lluís Revilla wrote:
| To solve it, it might be as simple as writing nimDim <- NULL inside your
| package or there might be a real issue there.
Or call utils::globalVariables(c("nimDim")) where, if needed, you could add
to that argument vector any other variables listed as global.
Cheers, Dirk
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Re: [R-pkg-devel] R Package Submission
It would be unusual these days to have pkg:ggplot as a dependency. — David. Sent from my iPhone > On Apr 5, 2025, at 10:28 AM, Paul Angelo Manlapaz > wrote: > > Dear Sir / Ma'am, > > Greetings. > > I am but a newbie in R Package development and currently, I am trying to > submit my second package to CRAN and every time after submission, the > results for the pre-tests come back 'does not pass the incoming checks > automatically'. > > The NOTE says; > > Possibly misspelled words in DESCRIPTION: >ProteinPCA (9:45, 12:19) >ggplot (12:5) > > The name of the package is ProteinPCA and I have already checked multiple > times the Description files for any possible misspellings but I have not > found any. Same goes with ggplot2. > > At this moment, I am really at loss on how to resolve this issue. Could you > perhaps enlighten me on this? > > Thank you very much. > > Sincerely, > *P. A. C. Manlapaz, RCh* > >[[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
