ComplexHeatmap crashing R session

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Hi Zuguang I have used ComplexHeatmap successfully several times in the past but recently I've been having an issue where the R session crashes when I try to plot a matrix with Heatmap(). Trying to troubleshoot a little bit I found that even a basic plot crashes the session. Reinstalling the package from Bioconductor or GitHub didn't work either. Any ideas on what might be causing this problem? Details below:

library(ComplexHeatmap) Loading required package: grid ======================================== ComplexHeatmap version 2.18.0 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:

• Gu, Z. Complex Heatmap Visualization. iMeta 2022.
• Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016.

The new InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap))

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.2.1

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

attached base packages: [1] grid stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] ComplexHeatmap_2.18.0

loaded via a namespace (and not attached): [1] digest_0.6.34 RColorBrewer_1.1-3 codetools_0.2-19
[4] GlobalOptions_0.1.2 circlize_0.4.15 shape_1.4.6
[7] doParallel_1.0.17 clue_0.3-65 rjson_0.2.21
[10] matrixStats_1.2.0 iterators_1.0.14 parallel_4.3.2
[13] BiocGenerics_0.48.1 png_0.1-8 stats4_4.3.2
[16] foreach_1.5.2 IRanges_2.36.0 compiler_4.3.2
[19] cluster_2.1.6 colorspace_2.1-0 S4Vectors_0.40.2
[22] crayon_1.5.2 GetoptLong_1.0.5

m = matrix(rnorm(100), 10) Heatmap(m)

*** caught segfault *** address 0x0, cause 'unknown'

Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 4: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 6: loadNamespace(package, ...) 7: doTryCatch(return(expr), name, parentenv, handler) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9: tryCatchList(expr, classes, parentenv, handlers) 10: tryCatch(loadNamespace(package, ...), error = function(e) e) 11: requireNamespace("magick", quietly = TRUE) 12: Heatmap(m)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection

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As pointed out in the answer to my question on Bioconductor forum the problem is related to the package magick. Not sure exactly what is triggering this segfault but removing magick it's a workaround.

https://support.bioconductor.org/p/9156439/