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

[Ahmed Mohamed]

Thanks Vincent.

I would like to debug the error, but I still cannot reproduce it.
SessionInfo, below, shows update to date versions! My Travis build also
works, with Bioc Devel and iheapmapr 0.4.12 (
https://travis-ci.org/github/ahmohamed/lipidr/jobs/696329028#L2718). What
am I missing?

> sessionInfo()R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=C
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils
datasets  methods
[9] base

other attached packages:
 [1] lipidr_2.3.0                SummarizedExperiment_1.19.5
DelayedArray_0.15.4
 [4] matrixStats_0.56.0          Matrix_1.2-18
Biobase_2.49.0
 [7] GenomicRanges_1.41.5        GenomeInfoDb_1.25.2
IRanges_2.23.10
[10] S4Vectors_0.27.12           BiocGenerics_0.35.4
iheatmapr_0.4.12
[13] BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] fastcluster_1.1.25     tidyselect_1.1.0       xfun_0.14
 [4] purrr_0.3.4            lattice_0.20-41        colorspace_1.4-1
 [7] vctrs_0.3.1            generics_0.0.2         htmltools_0.5.0
[10] yaml_2.2.1             rlang_0.4.6            pillar_1.4.4
[13] glue_1.4.1             RColorBrewer_1.1-2     GenomeInfoDbData_1.2.3
[16] lifecycle_0.2.0        plyr_1.8.6             zlibbioc_1.35.0
[19] munsell_0.5.0          gtable_0.3.0           htmlwidgets_1.5.1
[22] knitr_1.28             forcats_0.5.0          Rcpp_1.0.4.6
[25] scales_1.1.1           limma_3.45.7           jsonlite_1.6.1
[28] XVector_0.29.2         farver_2.0.3           ggplot2_3.3.1
[31] digest_0.6.25          dplyr_1.0.0            ropls_1.21.0
[34] grid_4.0.0             tools_4.0.0            bitops_1.0-6
[37] magrittr_1.5           RCurl_1.98-1.2         tibble_3.0.1
[40] ggdendro_0.1-20        tidyr_1.1.0            crayon_1.3.4
[43] pkgconfig_2.0.3        MASS_7.3-51.5          ellipsis_0.3.1
[46] data.table_1.12.8      rstudioapi_0.11        R6_2.4.1
[49] compiler_4.0.0


On Wed, 17 Jun 2020 at 20:12, Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> 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.
>>
>>         [[alternative HTML version deleted]]
>>
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