vector memory limit reached, see mem.maxVSize()

[ftencaten]

Hi,
I'm running into an issue when trying to plot the network:

> plotMsigNetwork(gs_ovnet) Error in ggraph::geom_edge_link(): ! Problem while converting geom to grob. ℹ Error occurred in the 1st layer. Caused by error: ! vector memory limit of 100.0 Gb reached, see mem.maxVSize() Run rlang::last_trace() to see where the error occurred.

This happens when I follow the tutorial or analyze my own data. Sometimes it works, depending on the number of pathways and the size of the network. I haven't tested extensively to see exactly when the network size starts to be a problem

Thanks for the help

`> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[6] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[11] vissE_1.14.0 GSEABase_1.68.0 graph_1.84.0 annotate_1.84.0 XML_3.99-0.18
[16] AnnotationDbi_1.68.0 IRanges_2.40.0 S4Vectors_0.44.0 Biobase_2.66.0 BiocGenerics_0.52.0
[21] msigdb_1.14.0

loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2 farver_2.1.2 blob_1.2.4 viridis_0.6.5
[6] filelock_1.0.3 Biostrings_2.74.0 ggraph_2.2.1 fastmap_1.2.0 BiocFileCache_2.14.0
[11] tweenr_2.0.3 timechange_0.3.0 mime_0.12 lifecycle_1.0.4 KEGGREST_1.46.0
[16] RSQLite_2.3.9 magrittr_2.0.3 compiler_4.4.2 rlang_1.1.5 tools_4.4.2
[21] igraph_2.1.4 yaml_2.3.10 knitr_1.49 labeling_0.4.3 graphlayouts_1.2.2
[26] bit_4.5.0.1 curl_6.2.0 plyr_1.8.9 RColorBrewer_1.1-3 withr_3.0.2
[31] grid_4.4.2 polyclip_1.10-7 ExperimentHub_2.14.0 xtable_1.8-4 colorspace_2.1-1
[36] scales_1.3.0 MASS_7.3-64 cli_3.6.3 crayon_1.5.3 generics_0.1.3
[41] rstudioapi_0.17.1 tzdb_0.4.0 httr_1.4.7 reshape2_1.4.4 DBI_1.2.3
[46] cachem_1.1.0 ggforce_0.4.2 zlibbioc_1.52.0 BiocManager_1.30.25 XVector_0.46.0
[51] vctrs_0.6.5 jsonlite_1.8.9 hms_1.1.3 ggrepel_0.9.6 bit64_4.6.0-1
[56] glue_1.8.0 stringi_1.8.4 gtable_0.3.6 BiocVersion_3.20.0 GenomeInfoDb_1.42.1
[61] UCSC.utils_1.2.0 munsell_0.5.1 pillar_1.10.1 rappdirs_0.3.3 GenomeInfoDbData_1.2.13
[66] R6_2.5.1 dbplyr_2.5.0 tidygraph_1.3.1 evaluate_1.0.3 AnnotationHub_3.14.0
[71] png_0.1-8 memoise_2.0.1 Rcpp_1.0.14 gridExtra_2.3 xfun_0.50
[76] pkgconfig_2.0.3 `

[ftencaten]

Not complete sure what exactly the issue is but replacing ggraph::geom_edge_link() by ggraph::geom_edge_link0() in the plotMsigNetwork function seems to be a workaround.