run_pathfindR function frozen

[sophie-harrington]

Hello,

I have just started using pathfindR, and after installing initially the package seemed to be working well. However, recently the run_pathfindR function seems to be stalling at the Active Subnetwork Search stage. I've tried to re-run gene sets which I know processed within ~30 min just a few days ago, and they're sitting at this stage of the process for 3+ hours before I kill the job.

Do you have any idea what might be causing this? I've tried re-installing the package, and that hasn't made a difference.

Session info is below.

Thanks!!

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] tidyr_1.1.4 dplyr_1.0.7 pathfindR_1.6.3
[4] pathfindR.data_1.1.2

loaded via a namespace (and not attached): [1] ggrepel_0.9.1 Rcpp_1.0.7 Biostrings_2.62.0
[4] png_0.1-7 digest_0.6.29 foreach_1.5.1
[7] utf8_1.2.2 ggforce_0.3.3 GenomeInfoDb_1.30.0
[10] R6_2.5.1 stats4_4.1.2 RSQLite_2.2.9
[13] evaluate_0.14 httr_1.4.2 ggplot2_3.3.5
[16] pillar_1.6.4 zlibbioc_1.40.0 rlang_0.4.12
[19] blob_1.2.2 S4Vectors_0.32.3 rmarkdown_2.11
[22] RCurl_1.98-1.5 igraph_1.2.11 polyclip_1.10-0
[25] bit_4.0.4 munsell_0.5.0 compiler_4.1.2
[28] xfun_0.29 pkgconfig_2.0.3 BiocGenerics_0.40.0
[31] htmltools_0.5.2 tidyselect_1.1.1 KEGGREST_1.34.0
[34] GenomeInfoDbData_1.2.7 tibble_3.1.6 gridExtra_2.3
[37] IRanges_2.28.0 codetools_0.2-18 graphlayouts_0.8.0
[40] fansi_0.5.0 viridisLite_0.4.0 crayon_1.4.2
[43] bitops_1.0-7 MASS_7.3-54 grid_4.1.2
[46] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[49] magrittr_2.0.1 scales_1.1.1 cachem_1.0.6
[52] XVector_0.34.0 farver_2.1.0 viridis_0.6.2
[55] doParallel_1.0.16 ellipsis_0.3.2 generics_0.1.1
[58] vctrs_0.3.8 org.Hs.eg.db_3.14.0 iterators_1.0.13
[61] tools_4.1.2 bit64_4.0.5 Biobase_2.54.0
[64] glue_1.6.0 tweenr_1.0.2 purrr_0.3.4
[67] ggraph_2.0.5 parallel_4.1.2 fastmap_1.1.0
[70] AnnotationDbi_1.56.2 colorspace_2.0-2 BiocManager_1.30.16
[73] tidygraph_1.2.0 memoise_2.0.1 knitr_1.37

[egeulgen]

Hello,

Is it running for longer with the same input? If you don't mind, can you share the input data frame as an RDS file (you can e-mail me at egeulgen [at] gmail.com)?

[sophie-harrington]

Hi,

Thanks for responding so quickly. Yes, it is slow with exactly the same input files which ran perfectly well earlier last week. I'm also testing the "RA_input" file provided through the package at the moment, and that has been running for 20 min with no results so far (though I don't know how long you would expect that to take).

I will email you an example RDS file shortly.

Thanks!