Remove recently archived CRAN packages from devel builders

[jwokaty]

https://cran.r-project.org/web/packages/assertive/index.html

[hpages]

Other packages that got removed from CRAN that affect us:

• norm2: https://cran.r-project.org/package=norm2
• corncob: https://cran.r-project.org/package=corncob
• uchardet: https://cran.r-project.org/package=uchardet

Note that we should also update kjohnson1 to R 4.3.2 so no need to remove anything there.

Thx!

[jwokaty]

Is there some process you used to figure out what dependencies were archived? I am waiting on the actual release for M1 as it is still the RC version.

[hpages]

Just spotted another one (archived on 2023-10-24):

• multipanelfigure: https://cran.r-project.org/package=multipanelfigure. Breaks celda + indirectly decontX and singleCellTK.

Is there some process you used to figure out what dependencies were archived?

Just poking around https://bioconductor.org/checkResults/3.19/bioc-LATEST/long-report.html and looking at merida1-only errors.

I am waiting on the actual release for M1

Seems to have landed (or taken off? :rocket: ): https://cran.r-project.org/bin/macosx/

[hpages]

One more (archived on 2023-10-29):

• rbokeh: https://cran.r-project.org/package=rbokeh. Breaks SeqSQC.

Darn, it's almost like CRAN decided to remove stuff right after we made a new release! :upside_down_face:

[hpages]

One more (archived on 2023-07-09):

• rsnps: https://cran.r-project.org/package=rsnps. Breaks appreci8R.

That should be all for now.

[jwokaty]

Seems to have landed (or taken off? 🚀 ): https://cran.r-project.org/bin/macosx/

Thanks. I always check mac.r-project.org, which currently shows RC.

Thanks for keeping track of the packages. Should we follow up with maintainers?

[lshep]

FWIW: MsCoreUtils, benchdamic and MMAPPR2 responded. autonomics/multicrispr and RCy3 have not responded. But those maintainers have been contacted already.

[hpages]

Thanks. I always check mac.r-project.org, which currently shows RC.

That's not the right place to check for an official R release.

[jwokaty]

That's not the right place to check for an official R release.

Noted. All release builders are updated.

[hpages]

Is there some process you used to figure out what dependencies were archived?

@jwokaty FWIW here is a little function you can use to find those CRAN packages that are installed on a builder but have vanished from CRAN:

find_vanished_CRAN_pkgs <- function(CRAN_repos="https://cran.r-project.org") {
    inst_pkgs <- installed.packages()[ , "Package"]
    is_cran <- sapply(inst_pkgs, function(pkg) "CRAN" %in% packageDescription(pkg)$Repository)
    inst_cran_pkgs <- inst_pkgs[is_cran]
    all_cran_pkgs <- available.packages(repos=CRAN_repos)[ , "Package"]
    setdiff(inst_cran_pkgs, all_cran_pkgs)
}

Returns the following on nebbiolo1:

> find_vanished_CRAN_pkgs()
 [1] "assertive.code"       "assertive.data"       "assertive.data.uk"   
 [4] "assertive.data.us"    "assertive.datetimes"  "assertive.properties"
 [7] "assertive.strings"    "assertive.types"      "multipanelfigure"    
[10] "optimr"               "rbokeh"               "Rcgmin"              
[13] "Rvmmin"              

We should probably think about having BBS automatically remove vanished packages (+ their rev deps) at the beginning of a run.

[jwokaty]

• [x] Check Ubuntu-files for dependencies related to removed CRAN packages