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 <st...@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 <moha...@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > The information in this e-mail is intended only for th...{{dropped:15}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
