ComplexHeatmap crashing R session
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0
Entering edit mode
Felipe • 0
@b018e9fe
Last seen 2 days ago
United States

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
ComplexHeatmap • 178 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

The error is occurring when loading the magick package, which may be broken. You could try loading that package in a clean R session to see if that is it, and if so you may need to reinstall.

0
Entering edit mode

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!

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