[Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)
Hi Ahmed, Just a heads up that Lori's workaround (reinstalling iheatmap from source on all the builders) should be considered a temporary one and that the fundamental problem remains. The fundamental problem being that the iheatmap's Windows and Mac binaries that are on CRAN are broken. And the reason they are broken is because they contain stale information in their method cache. As a consequence, the lipidr error you were seeing a few days ago on our build report is back today on the devel report: https://bioconductor.org/checkResults/3.12/bioc-LATEST/lipidr/ Note that this time it's only on Windows and Mac. This is because yesterday we updated R to R 4.0.2 on the devel builders so the build machines automatically reinstalled all the deps from scratch. iheatmap is one of them and the build system picked up the Windows and Mac binaries from CRAN, which are broken :-/ We'll see the same problem on the release builds when we update R to R 4.0.2 there too. Bottom line: the only true fix is that the iheatmap authors/maintainers upload a new version of their package to CRAN. The only change they need to do is bump the version. Alternatively, they could reconsider depending on S4Vectors. Bioconductor moves fast and CRAN packages that depend on Bioconductor packages are inherently at the risk of seeing their binaries become stale. Hope this helps, H.
On 6/22/20 04:50, Shepherd, Lori wrote:
I reinstalled iheatmap yesterday and it should be reflected in today's
(Mondays) report.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
------------------------------------------------------------------------
*From:* Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>
*Sent:* Monday, June 22, 2020 2:18 AM
*To:* Martin Morgan <mtmorgan.bioc at gmail.com>
*Cc:* Vincent Carey <stvjc at channing.harvard.edu>; Herv? Pag?s
<hpages at fredhutch.org>; bioc-devel <bioc-devel at r-project.org>; Shepherd,
Lori <Lori.Shepherd at RoswellPark.org>
*Subject:* Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly
from S4Vectors)
Excellent catch Martin.
I was able to confirm the issue using the script below (on Bioc-Devel
Docker). The issue was also resolved by simply reinstalling iheatmapr.
It would be great if iheatmapr is reinstalled manually on the devel
build systems.
remove.packages(c("iheatmapr", "S4Vectors"))
devtools::install_github("Bioconductor/S4Vectors",
ref="e8dffc0157f2c4779fce3c85e5ef601bb0a35d33")
install.packages("iheatmapr")
packageVersion("S4Vectors")
# "0.27.0"
packageVersion("iheatmapr")
# "0.4.12"
library(lipidr)
library(iheatmapr)
example("iheatmap")
# Runs successfully
## Update S4Vector
rm(list = ls())
rstudioapi::restartSession()
devtools::install_github("Bioconductor/S4Vectors")
packageVersion("S4Vectors")
# "0.27.12"
library(iheatmapr)
example("iheatmap")
# Error in .wrap_in_length_one_list_like_object(value, name, x) :
# ? failed to coerce 'list(value)' to a IheatmapPlots object of length 1
## Reinstall iheatmapr
rm(list = ls())
rstudioapi::restartSession()
install.packages("iheatmapr")
library(iheatmapr)
example("iheatmap")
# Runs successfully
Cheers.
Ahmed.
On Thu, 18 Jun 2020 at 00:52, Martin Morgan <mtmorgan.bioc at gmail.com
<mailto:mtmorgan.bioc at gmail.com>> wrote:
You can see package versions on the build system from
https://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
<https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1HWo5rIWA1m5ihxjEdHQES7eiiUCH5lqvmKOON4J2Nm8lJSd6ncmMQs2-5FhUktt5pXPTp1smrU6cKa4190T7elc944QS2Ydfuvp0t0c29VorU11a-5FJwrxBfbADYAfJGX5CDQJNzcBds5IVb-5FLtdmsg7t8Ld-5FJyXp3M7L7uW2MvmMMnH8ci3Phnzvw-5FiaOi0u9G-2Dl54dBJQI5av1sYcF-2DXB-2DchvqVtJ-5FdoIbdWZgo0cQbvpDTl4qwhMSI3-2DT5j57ghQcQiG5qiGemiudrobXzA6XqKDpvteiE2tnv1JEegc1WaEKcl6RRjDDR3DXUQOSDD-2Diwfdcr-5FfKL4y8BIfVSxVcfA9foqFw5ODRUoVPtzsaS0_https-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252Findex.html&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=HMLRRZSzTs8eBf-GQBqLOx4AlcpY2d5kNsLvFPq7SQY&e=>
clicking on 'installed pkgs' link in the center top table. iheatmapr
is at version 0.4.12.
I think what is happening is like
https://support.bioconductor.org/p/131689/#131695
<https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1CwyVIg3N8SoBBwdD-5FFZCiSutr81swQb4KYpE6AXzbu-2DD36e-5F5eSxfAEMhJSyL-2DJ7KoruFV35JklCfpumYnw-5FPV4SpILT4B7wuZtuwXsxnWJYFdapO9ukunWgWn39PwtvG1o5zkiJjv1wwLOio-2D63U40zo3qPGplTSe3XQN4LtamopYmUBwTYsEewP58hJ4qna2-2DBpptSChUQo998UFg55JhNHe8ejCjdB1IvVvZSikJx2zpcqfEQZ-2DkvLK-5FNcASuHZk8jVRxH9LtAiCXae2enWAZvaXxUDc-2D-5F0Oiov8GTnMdglDnbpl2KouhuA9-5F2xdNAvcsZwWynXeOmu0sJhz8GA_https-253A-252F-252Fsupport.bioconductor.org-252Fp-252F131689-252F-2523131695&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=3KVxHEJz2pfQnC1j0ujPEyZd4m4g6K_HYtqOooMmNKA&e=>
where S4Vector method has been changed but packages that use it have
a methods table that is cached when the package is installed.
So there are no errors if you do a new install of packages (like on
CI or the docker) but not if the iheatmapr package has already been
installed (as I guess on the build system).
This means that the only way to reproduce this would be to install a
previous version of S4Vectors, then install iheatmapr to capture the
old methods table, then install the current version of S4Vectors.
But at the end of the day the solution is (a) for iheatmapr to be
updated on the build systems and ideally (b) for iheatmapr to bump
it's version. A version bump would be trivial if it were a
Bioconductor package, but could be problematic for CRAN. I did bcc
the maintainer.
I don't think you should work around this (e.g., by disabling the
example) because, at least if it were me, I'd forget to reenable
this and hence end up with less extensive testing of my package (and
the overall Bioconductor ecosystem).
Maybe @Herv? Pag?s will chime in; my diagnosis could be wrong.
Martin
On 6/17/20, 6:56 AM, "Bioc-devel on behalf of Ahmed Mohamed"
<bioc-devel-bounces at r-project.org
<mailto:bioc-devel-bounces at r-project.org> on behalf of
mohamed at kuicr.kyoto-u.ac.jp <mailto:mohamed at kuicr.kyoto-u.ac.jp>> wrote:
? ? 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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__secure-2Dweb.cisco.com_1If8yOo3b-5FxBYYwzpHg-2Dc7ZSLnTAhugHgmCjgkxTHiPbgSmK-2DeSNwegV5ae-5Fl5VcGUe0rds-2Df7dFKtbjP7jCW1gpaFTioG1RhvwHy1xdrRWcQt-2DRqbT5PGC-5FIDlLdsQe132vjO1GjpChUt-5FK8tweNVhePXGcHlTmc-5FKOfzswdP-5F0X9YEmStFcons03ZGXW-2DlRS3oObzAeqSeuMiqJwarP6pM87LZPguM8Z6aotYwPlhBqwjaFubrbVbeQWJYtOkMXvOUzTo-2D0LaJAc1fhF7z-2DZNlnVXYTGY9b7Yh-2DOQrG9rQzucF3nO4J7jl48ZhfGNTuoNbb0e7opYwWBH7qWU-2Dptw_https-253A-252F-252Ftravis-2Dci.org-252Fgithub-252Fahmohamed-252Flipidr-252Fjobs-252F696329028-2523L2718&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=i4n6aBAm0IWMm11VV0AuKf-Jq61pEHvyTEZGu9MCpHE&e=>).
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
<https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1oB-2DH4JrlZ3Yw2PA1QlZgPu-2D-5FXEPyS21Qc6ieR-2DurRitGqbuk0Me344f9ma39c2DI9zAMJLdWApN4WESftimsVP0KegYiLOCcT8vFiUci3sKe0rUYtsktX5YSyEJXLBEt9y9ucaujFQYeZUdyqYdVcm94SMos00SQgQ6oK-5FPBNeHCk6ZnNtnKfoPhBQJ4Od-2DurXG9Y47nMj-5FURgWBajqf9spQcOmCUi9JWW6fbiPPcK1cDYYZ-2DgiE78iwi4fNHcQSJeltQd2s7VVYdbgj8Tmu-2DUW0evWQXfkqNWY7YFjVOlbLM1qiQ7s3VPbNtiv0BlhX_http-253A-252F-252Flibopenblasp-2Dr0.2.20.so&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=xNH-mluwP2TY76rL-3yFRqVFhl2nn1F9pzfXnWtuhuo&e=>
? ? 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 <mailto: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
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? ? >
? ? > 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
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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 <mailto: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
<https://urldefense.proofpoint.com/v2/url?u=http-3A__secure-2Dweb.cisco.com_1BmOiFuqUzjQClVteG9kNuRUbaCYyUKcVPJCpRdxSZP0gTKw8ameWB9wiERTs4z4PDu0QUk7LJm2OtnUAbfa1I4j5le5O8d07Gbm-5Farj2XtmSi7lZHl75jGmsThiQv-2DFeQUH0gDkZMb1RiNWpPJVd8-5FhN84qX8baWqAWsMFZv17HnyHwYSd9-2DznXCojeUOB7q26Ht-5FB-2D5sVwuAJS3uKTt7NuarJEkEJYKU9iQdGqcyPlKNjZfbJkB-5Fz-5FmLtmcP8IHBQIcFFw5x30MSqPtogb0jSShK0GCo9zcC6Y3EpsqMFfkFiwrti6ne5hwKWY-5FWW6lEAw5zaPZ-5FzADRAqJGOkAhjFLLUHt7nDJlEa59HTg3EM_http-253A-252F-252Fbioconductor.org-252FcheckResults-252Fdevel-252Fbioc-2DLATEST-252Flipidr-252Fmalbec1-2Dchecksrc.html&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=KMYCcC6SjfUiCjL5IgcN30_DGaTKHyt5xAmA2OaY-2s&s=Flv1K5xmBQs4Ul9Q0Kc62ea1zNaZ5fXNiOsiyudoF2Y&e=>
? ? >> )
? ? >>
? ? >> 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
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? ? >>
? ? >> Any suggestions would be appreciated.
? ? >> Thanks.
? ? >> Ahmed.
? ? >>
? ? >>? ? ? ? ?[[alternative HTML version deleted]]
? ? >>
? ? >> _______________________________________________
? ? >> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
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