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KlausVigo / phangorn

Phylogenetic analysis in R
http://klausvigo.github.io/phangorn/
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Phangorn removal warning from CRAN #111

Closed danlwarren closed 3 years ago

danlwarren commented 3 years ago

Hi Klaus! I just got an email from CRAN saying phangorn was going to be pulled in a couple of weeks if some issues weren't fixed (https://cran.r-project.org/web/checks/check_results_phangorn.html), and that RWTY will be pulled due to dependencies as well. Just wanted to check in with you and see if you are working on these, because we'll need to find a workaround if not.

Cheers!

dwbapst commented 3 years ago

If we look at the R CHECK output resulting from CRAN's automated checking, we see that the WARNING errors appear to occur with trying to build vignettes:

https://cran.r-project.org/web/checks/check_results_phangorn.html

https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64-gcc10-UCRT/phangorn-00check.html

checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
  ...
--- re-building 'AdvancedFeatures.Rmd' using rmarkdown
--- finished re-building 'AdvancedFeatures.Rmd'

--- re-building 'Ancestral.Rmd' using rmarkdown
Quitting from lines 57-59 (Ancestral.Rmd)
Error: processing vignette 'Ancestral.Rmd' failed with diagnostics:
there is no package called 'seqLogo'
--- failed re-building 'Ancestral.Rmd'

--- re-building 'IntertwiningTreesAndNetworks.Rmd' using rmarkdown
--- finished re-building 'IntertwiningTreesAndNetworks.Rmd'

--- re-building 'Networx.Rmd' using rmarkdown
--- finished re-building 'Networx.Rmd'

--- re-building 'Trees.Rmd' using rmarkdown
--- finished re-building 'Trees.Rmd'

SUMMARY: processing the following file failed:
  'Ancestral.Rmd'

Error: Vignette re-building failed.
Execution halted

It looks like the real problem is not being able to find seqLogo package in the Ancestral.Rmd vignette. So presumably removing the reference to that package in that vignette should allow phangorn to safely pass CRAN testing.

bomeara commented 3 years ago

seqLogo is in bioconductor -- has been for 14 years, last updated 5 months ago, and is still available at BioConductor. I don't see anything in the Writing R Extensions guide about using BioConductor packages in vignettes, but maybe this is now a problem.

KlausVigo commented 3 years ago

Hi all,

a new version is on the way to CRAN. It probably needs a day for the reverse dependency checks on their side, if everything works fine. On the other hand last time it was for 3 month in the loop. @bomeara, it used to be that vignettes could call suggested packages, that seems not the case any more or is enforced nowadays. Now I am not sure what suggested would be any good for.

I was pretty busy the last weeks moving flats and teaching so did not take Ripley's message serious enough. On the other hand it's ridiculous to set the dead line for on a holiday. As it was yesterday public holiday in Austria, where CRAN lives, so much for work-life balance in academia.

Regards, Klaus

dwbapst commented 3 years ago

Even disregarding that CRAN 'lives' in Austria (a concept that suggests that CRAN itself is an organism, in which case I do not want to know anything more about its biology, or appearance, or phylum), you'd think they'd give more time for a response during an ongoing global pandemic!

On Tue, Apr 6, 2021 at 7:15 AM Klaus Schliep @.***> wrote:

Hi all,

a new version is on the way to CRAN. It probably needs a day for the reverse dependency checks on their side, if everything works fine. On the other hand last time it was for 3 month in the loop. @bomeara https://github.com/bomeara, it used to be that vignettes could call suggested packages, that seems not the case any more or is enforced nowadays. Now I am not sure what suggested would be any good for.

I was pretty busy the last weeks moving flats and teaching so did not take Ripley's message serious enough. On the other hand it's ridiculous to set the dead line for on a holiday. As it was yesterday public holiday in Austria, where CRAN lives, so much for work-life balance in academia.

Regards, Klaus

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/KlausVigo/phangorn/issues/111#issuecomment-814071917, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAL5KLZNS24DNWQS4BYCFDDTHL3NBANCNFSM42NUXVZQ .

dwbapst commented 3 years ago

It looks like v2.6.3 is now on CRAN and so our nightmare can be over

https://cran.r-project.org/web/packages/phangorn/