Package ‘rgeos’ was removed from the CRAN repository.

[ahill187]

Description

The rgeos package was removed from the CRAN repository: https://cran.r-project.org/web/packages/rgeos/index.html. When I try to install flowDensity, I get this warning:

> BiocManager::install("flowDensity", force=TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'flowDensity'
Warning: dependency ‘rgeos’ is not available
trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-x86_64/contrib/4.3/flowDensity_1.34.0.tgz'
Content type 'application/x-gzip' length 6484119 bytes (6.2 MB)
==================================================
downloaded 6.2 MB

The install seems okay, but then when I try to load flowDensity, I get this error:

> library(flowDensity)
Error: package or namespace load failed for ‘flowDensity’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘rgeos’

Version/Software Info

I am currently using:

MacOSX: 12.13.1 Intel
R: 4.3.1

[mehrnoushmalek]

Hi Ainsleigh!
I'm not actively checking this repo, and haven't updated Bioconductor for a while, as I assumed someone else from our lab will take over.
I have created a develop branch, that doesn't have the rgeos dependency, but needs polyclip package.
You may want to install that one and see if it works for you.
I'm a bit easy but I can take a look later, if that doesn't solve your issue

[hpages]

Thanks @mehrnoushmalek for working on this. Any chance you can push your rgeos-free version of flowDensity to the Bioconductor git server at git.bioconductor.org? Note that both the RELEASE_3_18 and devel branches would need to be made rgeos-free.

We released Bioconductor 3.18 yesterday and flowDensity is part of it but unfortunately people won't be able to install it because of its dependency on rgeos.

Thank you for your contribution to Bioconductor!

H.

PS: See this reminder posted today on the Bioc-devel mailing list.

[mehrnoushmalek]

Hello @hpages, it's been a while that I'm not part of bioC, and won't be able to push the changes back. I have updated the master branch. I don't have any info on bioconductor git server.

[hpages]

@mehrnoushmalek Bioconductor transistioned from Subversion to git in 2017. See https://contributions.bioconductor.org/git-version-control.html for how to push changes to our git server.

Anyways, it's up to you if you still want to be involved with Bioconductor or not. Just be aware that if the package doesn't get fixed in Bioconductor, then we'll deprecate it and remove it.

Let us know what you want to do.

Best,
H.

[rsbivand]

This is the CMD check log for the code in this repo develop branch:
00check.log, with plenty of remaining problems, but not commected to the archiving of rgeos.

And this from the source repository https://www.bioconductor.org/packages/release/bioc/html/flowDensity.html:
00check.log, which would not inatall:

* installing *source* package 'flowDensity' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
Error in matchSignature(signature, fdef) : 
  more elements in the method signature (4) than in the generic signature (3) for function 'flowDensity'
Error: unable to load R code in package 'flowDensity'
Execution halted
ERROR: lazy loading failed for package 'flowDensity'
* removing '/home/rsb/topics/packages/github-rsb/flowDensity.Rcheck/flowDensity'

So a new maintainer is need urgently, I think.

[mehrnoushmalek]

The above error should be fixed in the master branch.

[rsbivand]

Thanks. In master here now:
00check.log

[mehrnoushmalek]

Thanks. In master here now: 00check.log

Did it work for you? Cause I cannot see any error in the log you shared.

[rsbivand]

There are four warnings, all of which are potentially serious. In general, only clearly harmless NOTEs are acceptable, all warnings should be fixed, I believe, I think Bioconductor and CRAN do the same @hpages ?

[mehrnoushmalek]

I fixed some, but I'm not sure how S4-method documentation warning goes away. They all show up when testing with ?, so I'm not sure what causes it, and if it's too much effort. I won't be able to do it.
This package was approved by BioConductor with these warnings before, so if the policy has changed, I won't be able to catch-up with new polices.

[hpages]

Speaking for Bioconductor only: ideally all warnings should be fixed, but some exceptions can be made. In any case the warnings should not be a showstopper for pushing the changes to Bioconductor. They are a lesser problem compared to Bioconductor users not being able to install the package or any of its reverse deps at the moment.

If you ever decide to push this to Bioconductor, our daily build/check report will simply report these warnings, and they can always be taken care of later by subsequent pushes.

Thanks