Generating ion images - "R encountered a fatal error"

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Matthew Smith

Jan 10, 2024, 4:51:14 AMJan 10
to Cardinal MSI Help

Enjoying continually using the package.

I have encountered a recurring error - "R encountered a fatal error".

This occurs when generating ion images, with for instance:
  • Cardinal::image(tissue, contrast.enhance="histogram", smooth.image = 'gaussian', superpose = FALSE, normalize.image = "linear", feature =fData(tissue)@mz[1:nrow(fData(tissue))])
  • Cardinal::image(tissue, contrast.enhance="histogram", smooth.image = 'gaussian', superpose = FALSE, normalize.image = "linear", feature =fData(tissue)@mz[5])
Has anyone else encountered this?

session info:

R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8 time zone: Europe/Stockholm tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] quantMSImageR_0.0.1.0 chemCal_0.2.3 dplyr_1.1.3 Cardinal_3.2.1 S4Vectors_0.38.2 EBImage_4.42.0 BiocParallel_1.34.2 [8] BiocGenerics_0.46.0 ProtGenerics_1.32.0 loaded via a namespace (and not attached): [1] utf8_1.2.3 generics_0.1.3 tiff_0.1-11 bitops_1.0-7 jpeg_0.1-10 lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 [9] evaluate_0.22 grid_4.3.0 fftwtools_0.9-11 fastmap_1.1.1 Matrix_1.6-1.1 matter_2.2.0 DBI_1.1.3 mclust_6.0.0 [17] biglm_0.9-2.1 fansi_1.0.5 viridisLite_0.4.2 codetools_0.2-19 abind_1.4-5 cli_3.6.1 rlang_1.1.1 Biobase_2.60.0 [25] yaml_2.3.7 tools_4.3.0 parallel_4.3.0 locfit_1.5-9.8 vctrs_0.6.3 R6_2.5.1 png_0.1-8 lifecycle_1.0.3 [33] htmlwidgets_1.6.2 MASS_7.3-60 irlba_2.3.5.1 pkgconfig_2.0.3 pillar_1.9.0 glue_1.6.2 tidyselect_1.2.0 tibble_3.2.1 [41] xfun_0.39 rstudioapi_0.15.0 knitr_1.44 htmltools_0.5.6 nlme_3.1-163 rmarkdown_2.25 signal_0.7-7 compiler_4.3.0 [49] RCurl_1.98-1.12 sp_2.1-0

Matthew Smith

Jan 17, 2024, 8:45:24 AMJan 17
to Cardinal MSI Help
In case anyone experiences a similar issue, I found out this was related to the memory available on my PC (so not related to Cardinal).
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