[R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Sat Sep 24 22:38:22 CEST 2022 

Hello. It looks like things to have changed since;

$ R CMD check --as-cran wflo_1.6.tar.gz
* using log directory ‘/tmp/wflo.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘wflo/DESCRIPTION’ ... OK
* this is package ‘wflo’ version ‘1.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ...^[O WARNING
Maintainer: ‘Carsten Croonenbroeck <carsten.croonenbroeck using uni-rostock.de>’

New submission

Package was archived on CRAN

Insufficient package version (submitted: 1.6, existing: 1.6)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2021-12-20 as requires archived package
    'emstreeR'.

Uses the superseded packages: ‘doSNOW’, ‘snow’

Found the following (possibly) invalid URLs:
  URL: https://www.researchgate.net/publication/2560062_Real-Time_Fluid_Dynamics_for_Games
    From: man/ShowWakePenalizers.Rd
    Status: 403
    Message: Forbidden

The Date field is over a month old.

This build time stamp is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wflo’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘wflo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cost
> ### Title: Stub for a turbine's cost function.
> ### Aliases: Cost
> ### Keywords: Cost Profit
>
> ### ** Examples
>
> ## Returns a vector of two, c(100000, 100000).
> Cost(c(0.5, 0.7), c(0.2, 0.3))
[1] 1e+05 1e+05
>
> ## Replace the function by another function
> ## also called 'Cost', embedded in environment e.
> ## Also, see the vignette.
> ## No test:
> e$Cost <- function(x, y) #x, y \in R^n
+ {
+     retVal <- rep(e$FarmVars$UnitCost, min(length(x), length(y)))
+     retVal[x > 0.5] <- retVal[x > 0.5] * 2
+     return(retVal)
+ }
> set.seed(1357)
> Result <- pso::psoptim(par = runif(NumTurbines * 2), fn = Profit,
+   lower = rep(0, NumTurbines * 2), upper = rep(1, NumTurbines * 2))
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'par' in selecting a method for
function 'psoptim': object 'NumTurbines' not found
Calls: <Anonymous> -> runif -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/tmp/wflo.Rcheck/00check.log’
for details.

So, you'll need to fix those in order for the package to reappear on CRAN.

My $.02

/Henrik

On Sat, Sep 24, 2022 at 12:15 PM Carsten Croonenbroeck
<carsten.croonenbroeck using uni-rostock.de> wrote:
>
> Dear Lluís, dear Ben,
>
> sorry about being close to impolite before, as you clearly have sensed ("as polite a request as you can manage"... :-)). I have cooled down a little bit by now and am currently processing the package to be resubmitted, but honestly, if this turns out to be as painful as it has been the first time, I will likely drop it half way through.
>
> Best wishes, and thanks and sorry again
>
> Carsten
>
>
> -----Ursprüngliche Nachricht-----
> Von: R-package-devel [mailto:r-package-devel-bounces using r-project.org] Im Auftrag von Lluís Revilla
> Gesendet: Donnerstag, 22. September 2022 23:22
> Cc: r-package-devel using r-project.org
> Betreff: Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.
>
> Hi,
>
> I would still submit the package:
> First I agree with Ben that the note is worth fixing (and easily enough you just need to remove rgdal from your Description if it is not used.) Second, and more important, because perhaps in the 9 months since the last check changes in r-devel or quality checks might currently cause the package to fail the checks.
>
> The idea behind CRAN, and packages repositories like it (Bioconductor), is that packages in them should work together.
> Sometimes this makes it easier for developers to write more complex packages but dependencies have their own cost such as this situation.
> You can share your package via other methods but usually users install packages from repositories.
>
> Cheers,
>
> Lluís
>
>
> On Thu, 22 Sept 2022 at 22:25, Ben Bolker <bbolker using gmail.com> wrote:
>
> >    * Automatic unarchiving *might* happen because someone on the CRAN
> > team happens to read this thread, but you will improve your odds
> > greatly by e-mailing cran using r-project.org with as polite a request as
> > you can manage ...
> >
> >   * My guess is that nothing will happen until you resubmit (FWIW the
> > NOTE definitely seems like something CRAN would object to, so you
> > should fix it before resubmitting ...)
> >
> >    good luck,
> >     Ben Bolker
> >
> > On 9/22/22 4:15 PM, Carsten Croonenbroeck wrote:
> > > Hi Lluís,
> > >
> > > thanks for the clarification. And kudos to your detective flair. I’m
> > serious about that, as I would never have found out about this chain
> > of events.
> > >
> > > Well, there are no error or warnings to fix, so I think it would be
> > > best
> > if someone from the CRAN team could “unarchive” wflo since there is no
> > problem there and none of the events that were set in motion were due
> > to any of my doings. Actually, I don’t really agree to have to
> > resubmit, and my time for doing so is very limited. Maybe in the next few weeks or so.
> > >
> > > Best
> > >
> > > Carsten
> > >
> > >
> > > Von: Lluís Revilla [mailto:lluis.revilla using gmail.com]
> > > Gesendet: Donnerstag, 22. September 2022 15:33
> > > An: Carsten Croonenbroeck
> > > Cc: r-package-devel using r-project.org
> > > Betreff: Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN
> > repository.
> > >
> > > Hi Carsten,
> > >
> > > This seems to be an unfortunate chain of events between different
> > packages: RcppMLPACK -> emstreeR -> wflo
> > >
> > > Package RcppMLPACK was archived on 2021-12-20 as issues were not
> > corrected despite reminders.
> > > This resulted in the package emstreeR being archived on 2021-12-20
> > > as
> > requires archived package 'RcppMLPACK'.
> > > Which also resulted in your package, wflo, being archived.
> > > Later, emstreeR was unarchived on 2022-03-21 after a successful
> > submission improving the dependencies (probably removing the
> > dependency to RcppMLPACK).
> > > You can see the source of this info on
> > https://cran.r-project.org/src/contrib/PACKAGES.in
> > >
> > > About the emails, usually maintainers whose package depends on a
> > > package
> > that is about to be removed receive an email with a date by which they
> > should fix the problems.
> > > But, as I am not part of the CRAN team I cannot check it.
> > >
> > > I would recommend preparing a new submission with all the errors and
> > warnings fixed.
> > > Note that I think the package will be checked as a new package.
> > >
> > > Best,
> > >
> > > Lluís
> > >
> > >
> > >
> > >
> > >
> > > On Thu, 22 Sept 2022 at 13:17, Carsten Croonenbroeck <
> > carsten.croonenbroeck using uni-rostock.de<mailto:
> > carsten.croonenbroeck using uni-rostock.de>> wrote:
> > > Hi,
> > >
> > > I was really, really, really surprised to learn today that my
> > > package
> > “wflo” was removed from CRAN almost a year ago!
> > >
> > > Telling from the output at https://CRAN.R-project.org/package=wflo,
> > this is due to my package being “Archived on 2021-12-20 as requires
> > archived package 'emstreeR'.” However, emstreeR is in no way archived
> > (see https://CRAN.R-project.org/package=emstreeR). Clicking “check
> > results archive”, it says that there is only a note
> > >
> > > Result: NOTE
> > >      Namespace in Imports field not imported from: ‘rgdal’
> > >       All declared Imports should be used.
> > >
> > > which is indeed correct, I don’t use rgdal anymore. What now, remove
> > > the
> > rgdal import and resubmit? How come I wasn’t informed, my E-Mail is
> > running perfectly. Very puzzling…
> > >
> > > Best
> > >
> > > Carsten
> > >
> > >          [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org<mailto:R-package-devel using r-project.org>
> > mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> > --
> > Dr. Benjamin Bolker
> > Professor, Mathematics & Statistics and Biology, McMaster University
> > Director, School of Computational Science and Engineering Graduate
> > chair, Mathematics & Statistics
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>         [[alternative HTML version deleted]]
>
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>
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