dependency on retiring spatial infrastructure packages through PopGenReport

[rsbivand]

See and fix https://github.com/green-striped-gecko/PopGenReport/issues/8

[mijangos81]

Hi,

we have removed all dartR’s dependencies on rgdal, rgeos, and/or maptools

Cheers, Luis

[rsbivand]

Please look to submit soon, as maptools 1.1-7 at https://r-forge.r-project.org/R/?group_id=943 is being submitted, and your package refers to elide which has moved to sp (HEAD of edzer/sp@main).

[rsbivand]

dartR@master and dartR@dev both still fail for sp 1.6-1 submitted to CRAN and maptools 1.1-7 (on CRAN) - dev: 00check.log

I am not at all impressed by your copying of my code from maptools/R/elide.R without attribution or permission.

I suggest that you condition on the versions of sp and maptools, simply re-instate the earlier code, or wait until sp 1.6-1 is on CRAN with the existing code, require sp >= 1.6-1 and drop maptools completely.

[mijangos81]

Dear Prof. Bivand,

Please receive my apologies for not properly attributing your code. I have removed the code from your elide function from our package. We will require sp >= 1.6-1 and reinstate our original code as you suggest. We will submit our package to CRAN as soon as possible.

Cheers, Luis

[rsbivand]

Please check that sp 1.6-1 is on CRAN first, buut do run local checks with that version of sp from edzer/sp, not CRAN if not yet available there. Do run local checks, devtools will not give convenient control of upstream package versions.

[rsbivand]

Time to submit: https://cran.r-project.org/web/checks/check_results_dartR.html.

[green-striped-gecko]

Time to submit: https://cran.r-project.org/web/checks/check_results_dartR.html.

Dear Prof Bivand, thanks for your timely reminder. We are very close to submit, just one dependency (ggtern) has to be resolved.

Kind regards, Bernd

[rsbivand]

OK, I see that it was archived for not fixing problems in a timely fashion. Please don't wait for ggtern to be fixed. If ggtern is essential, consider asking CRAN if you could submit a non-maintainer update (NMU) of ggtern, as the problems look clear, 4.3 made scalar logical tests of obects longer than one element a warning. Run CMD check on a local fork of ggtern to see if the issues are simple to fix or not. An NMU may be simplest, and would show CRAN thst you are contributing over and beyond dartR.

[rsbivand]

With https://cran.r-project.org/src/contrib/Archive/ggtern/ggtern_3.4.1.tar.gz and these replacements, ggtern.zip, it passes CMD check --as-cran. There is a badly formatted \Sexpr in line 15 of R/theme-elements.R - I just removed the backslash to stop Sexpr running. If replacing ggtern needs more time, consider an NMU. The package maintainer is unresponsive, http://www.ggtern.com/ suggests it hasn't been updated for a long time - wordpress errors. So longer-term, find a replacement, but try an NMU if you can't find a replacement in the short term. Maybe try to find others in the same state (tools::available.packages() and search in "Depends", "Imports" - maybe others - to see what they are doing. If dartR is the only affected reverse dependency, this is harder, if there are more, ask CRAN to orphan ggtern and appeal for a new maintainer. I think three packages: dartR, vdar and BloodCancerMultiOmics2017 suggest ggtern, so probably better to look for an alternative, probably https://cran.r-project.org/package=Ternary is a better choice than https://cran.r-project.org/package=isopleuros because the latter uses akima which has a very awkward license. Further, https://github.com/nicholasehamilton/ggtern/issues shows no movement at all for years.

[green-striped-gecko]

Hi Roger,

Thanks for the support and help. Can you please direct me what an NMU is.

Thanks again, Bernd

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From: Roger Bivand @.> Sent: Monday, 5 June 2023 22:47 To: green-striped-gecko/dartR @.> Cc: Bernd Gruber @.>; Comment @.> Subject: Re: [green-striped-gecko/dartR] dependency on retiring spatial infrastructure packages through PopGenReport (Issue #604)

With https://cran.r-project.org/src/contrib/Archive/ggtern/ggtern_3.4.1.tar.gz and these replacements, ggtern.ziphttps://github.com/green-striped-gecko/dartR/files/11652580/ggtern.zip, it passes CMD check --as-cran. There is a badly formatted \Sexpr in line 15 of R/theme-elements.R - I just removed the backslash to stop Sexpr running. If replacing ggtern needs more time, consider an NMU. The package maintainer is unresponsive, http://www.ggtern.com/http://www.ggtern.com/ suggests it hasn't been updated for a long time - wordpress errors. So longer-term, find a replacement, but try an NMU if you can't find a replacement in the short term. Maybe try to find others in the same state (tools::available.packages() and search in "Depends", "Imports" - maybe others - to see what they are doing. If dartR is the only affected reverse dependency, this iis harder, if there are more, ask CRAN to orphan ggtern and appeal for a new maintainer.

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[rsbivand]

Non-Maintainer Update.If you like, I could try to approach CRAN team about this.

[mijangos81]

Hi Prof. Roger,

Thank you for your support!

We are thinking about sending the below e-mail.

Regards, Luis

Dear CRAN Team,

I am writing to kindly request a Non-Maintainer Update (NMU) for the ggtern package (https://cran.r-project.org/src/contrib/Archive/ggtern/). Our package (dartR) and other two CRAN packages (PopGenHelpR and vdar) depends on ggtern. We have tried to contact ggtern's maintainer without success.

GGtern is an essential package for ternary diagram plotting in R, providing a powerful and flexible tool for visualizing data in three dimensions. However, the current version on CRAN is failing and has been archived.

Thank you for considering my request. I look forward to hearing from you and discussing the possibility of a Non-Maintainer Update for ggtern on CRAN.

Best regards,

[rsbivand]

Please consider adding "We need to update our packages because of ongoing changes in the sp package prior to the retirement of maptools, rgdal and rgeos." and adding roger.bivand@ nhh.no as CC.

[green-striped-gecko]

Hi Roger, thanks for your support, highly appreciated. ggtern seems to be back on CRAN and we aim to submit today once we have passed all tests. All the best, Bernd

[rsbivand]

Thanks. There is still the problem that PopGenReport imports rgdal, so dartR will not install when rgdal is not on the library path, because PopGenReport cannot be loaded without it. https://github.com/green-striped-gecko/PopGenReport/issues/8

[rsbivand]

@green-striped-gecko dartRwill not install whenrgdalis not on the library path, becausePopGenReport` cannot be loaded without it. https://github.com/green-striped-gecko/PopGenReport/issues/8

[rsbivand]

@green-striped-gecko A residual problem: dartR.base suggests maptools, which was archived yesterday. Please do move to submit an updated version as soon as possible.