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

Wed, Jun 17, 2020 3:56 AM

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?

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

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