[Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

[Vincent Carey]

I can reproduce the error, which arises from iheatmapr.  Note that

http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec1-R-instpkgs.html

shows that iheatmapr is 0.4.12 and on my system example(iheatmap) fails
with the
error you showed.  In future please provide sessionInfo() result when
reporting a
problem.

on my system, example(iheatmap) dies in an unexported function
main_heatmap.  iheatmapr is an ropensci
package that depends on S4Vectors.  it may only be tested with the release
version.  You
can see at https://travis-ci.org/github/ropensci/iheatmapr/jobs/698340792 that
iheatmapr
is passing its tests.  i don't know how to determine what packages were
used in the tests.

you might want to condition out your example for now.  perhaps you can
debug iheatmapr against
current S4Vectors and suggest the solution to iheatmapr authors


On Wed, Jun 17, 2020 at 1:26 AM Ahmed Mohamed <mohamed using kuicr.kyoto-u.ac.jp>
wrote:

> Hi all,
>
> My package "lipidr" has been failing checks for a while, giving the error
> below:
>
> Error in .wrap_in_length_one_list_like_object(value, name, x) :
>   failed to coerce 'list(value)' to a IheatmapPlots object of length 1
>
> (Full report here:
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/lipidr/malbec1-checksrc.html
> )
>
> The error seems to originate from S4Vectors package, which lipidr depends
> on (indirectly through SummarizedExperiment). However, I am completely
> unable to reproduce this error. This is what I did:
> - Installed Bioc-devel docker image
> - run the faulty example alone, as well as devtools::check(), both without
> errors.
> - Ran BiocManager::install(update = TRUE) to pick up updates not propagated
> to the docker image
> - I even installed S4Vector from GitHub, just in case the git checkout is
> ahead of Bioc.
>
> Faulty example:
> https://github.com/ahmohamed/lipidr/blob/master/R/plot.R#L345
>
> Any suggestions would be appreciated.
> Thanks.
> Ahmed.
>
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>
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