[R-pkg-devel] crowdsourcing/help with

[Henrik Bengtsson]

FWIW, you might want to do

loadNamespace("TMB")
library("TMB")

as loadNamespace() may give more informative error messages, cf.
https://github.com/HenrikBengtsson/Wishlist-for-R/issues/26.

Henrik


On Thu, Mar 10, 2022, 06:51 Ben Bolker <bbolker using gmail.com> wrote:

>    The win-builder output is here:
> https://win-builder.r-project.org/ce55MsIkho3o/00check.log
>
>    Key points:
>
>   the Anova.glmmTMB example fails, but this is the only output provided:
>
>  >
>  > ### ** Examples
>  >
>  > warp.lm <- glmmTMB(breaks ~ wool * tension, data = warpbreaks)
>  > salamander1 <-
>
> up2date(readRDS(system.file("example_files","salamander1.rds",package="glmmTMB")))
>
>   (I was wrong that examples fail immediately:
>
> https://win-builder.r-project.org/ce55MsIkho3o/examples_and_tests/glmmTMB-Ex.Rout
> shows that some examples do succeed)
>
>     I will try to make a test-A.R that runs first that *only* runs
> up2date (which is pretty much just a call to TMB::MakeADFun).  I might
> try a call to library(TMB), which might (?) throw an informative warning
> about a Matrix/TMB binary mismatch ...
>
>    thanks
>    Ben
>
>
>
> On 3/10/22 3:19 AM, Tomas Kalibera wrote:
> >
> > On 3/10/22 01:38, Ben Bolker wrote:
> >>
> >>   We (the glmmTMB developers) are having a hard-to-reproduce problem
> >> on Windows.  When run on CRAN's check platform or win-builder with
> >> r-devel, the code fails on the first example, when trying to
> >> reconstruct a 'TMB' object (TMB is a C++-based package we depend on).
> >> The problem is that we can't find a Windows system *other* than
> >> win-builder on which it fails -- it works on r-hub, and with 2 or 3
> >> other Windows 10/11 systems we've tried it on.
> >>
> >>   I suspect this has to do with an incompatibility in the binary stack
> >> - there is a dependency chain Matrix → TMB → glmmTMB, and we know that
> >> weird stuff can happen if the stack is incompatible (e.g. TMB was
> >> built with an older version of Matrix than is currently installed),
> >> but haven't managed to put together a stack that fails.
> >>
> >>   If anyone with a Windows system handy would be willing to try this
> >> out and see if it works that would be *super* handy (especially if you
> >> can get it to fail!)
> >>
> >>   You can read all about it here:
> >>
> >> https://github.com/glmmTMB/glmmTMB/issues/787
> >>
> >>    If you just want to grab the tarball so you can run R CMD check on
> >> it, try:
> >>
> >> r <- remotes::remote_download(github_remote("glmmTMB/glmmTMB/glmmTMB"))
> >> file.rename(r, "my_glmmtmb_tarball.tar.gz")
> >>
> >>    If you do manage to get it to fail, it would be great to see
> >> detailed output from
> >>
> >> library(glmmTMB)
> >>
> up2date(readRDS(system.file("example_files","salamander1.rds",package="glmmTMB")))
>
> >>
> >>
> >>   Any other debugging/diagnostic suggestions are of course welcome.
> >>   (If this fails we will probably have to put "skip if on Windows"
> >> logic around most of our examples and tests.)
> >
> > As you have a machine where it fails, which is winbuilder, could you
> > perhaps instrument your package to print the information you need to
> > debug the issue, and re-submit it? Also, to get more specific advice,
> > perhaps you could paste the actual output or a link to it.
> >
> > Best
> > Tomas
> >
> >>
> >>   cheers
> >>     Ben Bolker
> >>
> >> ______________________________________________
> >> 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
> (Acting) Graduate chair, Mathematics & Statistics
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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