here's my sessionInfo() -- we don't even agree on lipidr version. I presently don't have enough disk space to work on both devel and release so I work only on devel branch. I'll ask you to look over the different package versions and see if you can get closer to mine and then fail to generate error on example(plot_heatmap) .... check BiocManager::valid()
> sessionInfo() R version 4.0.1 beta (2020-05-28 r78607) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] lipidr_2.3.2 SummarizedExperiment_1.19.5 [3] DelayedArray_0.15.4 matrixStats_0.56.0 [5] Matrix_1.2-18 Biobase_2.49.0 [7] GenomicRanges_1.41.5 GenomeInfoDb_1.25.2 [9] IRanges_2.23.10 S4Vectors_0.27.12 [11] BiocGenerics_0.35.4 rmarkdown_2.2 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_0.4.0 [10] rlang_0.4.6 startup_0.14.1 pillar_1.4.4 [13] glue_1.4.1 RColorBrewer_1.1-2 plyr_1.8.6 [16] GenomeInfoDbData_1.2.3 lifecycle_0.2.0 zlibbioc_1.35.0 [19] munsell_0.5.0 gtable_0.3.0 htmlwidgets_1.5.1 [22] codetools_0.2-16 evaluate_0.14 knitr_1.28 [25] forcats_0.5.0 iheatmapr_0.4.12 Rcpp_1.0.4.6 [28] scales_1.1.1 limma_3.45.7 jsonlite_1.6.1 [31] XVector_0.29.2 ggplot2_3.3.1 digest_0.6.25 [34] dplyr_1.0.0 ropls_1.21.0 grid_4.0.1 [37] tools_4.0.1 bitops_1.0-6 magrittr_1.5 [40] RCurl_1.98-1.2 tibble_3.0.1 crayon_1.3.4 [43] tidyr_1.1.0 pkgconfig_2.0.3 ellipsis_0.3.1 [46] data.table_1.12.8 R6_2.4.1 compiler_4.0.1 On Wed, Jun 17, 2020 at 6:56 AM Ahmed Mohamed <moha...@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). 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 the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance HelpLine >> at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > -- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
