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I have used ComplexHeatmap several times in the past but recently I'm having this issue where the R session crashes when I try to plot any matrix with Heatmap(). Even a basic intro plot like the one in the example below creates a segfault. Reinstalling the package from Bioconductor or directly from GitHub repo didn't work either. Any ideas on what might be causing this problem?
> 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))
========================================
> 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:
> sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] digest_0.6.34 RColorBrewer_1.1-3 utf8_1.2.4 R6_2.5.1
[5] fastmap_1.1.1 xfun_0.41 tidyselect_1.2.0 magrittr_2.0.3
[9] glue_1.7.0 tibble_3.2.1 knitr_1.45 htmltools_0.5.7
[13] pkgconfig_2.0.3 rmarkdown_2.25 dplyr_1.1.4 generics_0.1.3
[17] lifecycle_1.0.4 cli_3.6.2 fansi_1.0.6 grid_4.3.2
[21] vctrs_0.6.5 compiler_4.3.2 rstudioapi_0.15.0 tools_4.3.2
[25] evaluate_0.23 pillar_1.9.0 yaml_2.3.8 rlang_1.1.3
oh I missed the reference to the magick package in the error message. Heatmap function worked fine after removing the package but created the same segfault after reinstalling it. For now, I'll just uninstall magick from my system. Thanks for the help James!