Error, cannot open the file connection

[travis-m-blimkie]

Describe the bug
When using run_pathfindR with the attached input genes, I receive an error that the function cannot open a file connection, when creating the subnetwork visualizations. I am able to run the function without issue using other input gene lists.

To reproduce:

1. Use the attached gene list as input
2. Run the following function:

run_pathfindR(
  input_genes,
  gene_sets  = "Reactome",
  output_dir = "PathfindR_results/",
  iterations = 5
)

3. See the following output/error:

## Testing input
The input looks OK
## Processing input. Converting gene symbols,
          if necessary (and if human gene symbols provided)
Number of genes provided in input: 8426
Number of genes in input after p-value filtering: 8426
pathfindR cannot handle p values < 1e-13. These were changed to 1e-13

Could not find any interactions for 958 (12.75%) genes in the PIN
Final number of genes in input: 6548
## Performing Active Subnetwork Search and Enrichment
## Processing the enrichment results over all iterations
## Annotating involved genes and visualizing enriched terms
Error in file(con, "wb") : cannot open the connectionadditional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain                                                                                                                                                                                                          
In addition: Warning messages:
1: Duplicated genes found! The lowest p value for each gene was selected 
2: In file(con, "wb") :
  cannot open file 'term_visualizations/TP53_regulates_transcription_of_several_additional_cell_death_genes_whose_specific_roles_in_p53-dependent_apoptosis_remain_uncertain.png': No such file or directory

Expected behavior:
As with other input gene lists, I should get a series of png files with subnetwork visualizations.

Screenshot:

Desktop:

• OS: Windows 10
• Development (github) version of pathfindR, 1.6.0.9004

R Session Information:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

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

other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[7] tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0 tRavis_0.65.00 pathfindR_1.6.0.9004 pathfindR.data_1.1.0

loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.9 bit64_4.0.5 doParallel_1.0.16 httr_1.4.2 tools_4.0.3
[7] backports_1.1.10 R6_2.4.1 DBI_1.1.0 BiocGenerics_0.34.0 colorspace_1.4-1 withr_2.3.0
[13] tidyselect_1.1.0 gridExtra_2.3 bit_4.0.4 compiler_4.0.3 cli_2.1.0 rvest_0.3.6
[19] Biobase_2.48.0 xml2_1.3.2 scales_1.1.1 digest_0.6.26 rmarkdown_2.4 pkgconfig_2.0.3
[25] htmltools_0.5.0 dbplyr_1.4.4 import_1.2.0 rlang_0.4.8 readxl_1.3.1 rstudioapi_0.11
[31] RSQLite_2.2.1 farver_2.0.3 generics_0.0.2 jsonlite_1.7.1 magrittr_1.5 Rcpp_1.0.5
[37] munsell_0.5.0 S4Vectors_0.26.1 fansi_0.4.1 viridis_0.5.1 lifecycle_0.2.0 stringi_1.5.3
[43] ggraph_2.0.3 MASS_7.3-53 org.Hs.eg.db_3.11.4 grid_4.0.3 blob_1.2.1 parallel_4.0.3
[49] ggrepel_0.8.2 crayon_1.3.4 graphlayouts_0.7.0 haven_2.3.1 hms_0.5.3 magick_2.5.0
[55] knitr_1.30 pillar_1.4.6 igraph_1.2.6 codetools_0.2-16 stats4_4.0.3 reprex_0.3.0
[61] glue_1.4.2 evaluate_0.14 modelr_0.1.8 vctrs_0.3.4 tweenr_1.0.1 foreach_1.5.1
[67] cellranger_1.1.0 gtable_0.3.0 polyclip_1.10-0 assertthat_0.2.1 xfun_0.18 ggforce_0.3.2
[73] broom_0.7.1 tidygraph_1.2.0 viridisLite_0.3.0 iterators_1.0.13 IRanges_2.22.2 tinytex_0.26
[79] AnnotationDbi_1.50.3 memoise_1.1.0 ellipsis_0.3.1

Additional context:
I am on java runtime 1.8.0_141
I have been able to successfully run the function by setting visualize_enriched_terms = FALSE, which implies the issue is with the visualization/file saving step.

Input file:
input_genes.txt

Any help would be greatly appreciated. Thanks!

[egeulgen]

hello @travis-m-blimkie,

can you make sure you have write privileges in the output directory?

I'm trying to reproduce the issue (but I'm on a mac) and will let you know if I can pinpoint the issue. I think it might be because of the long file name or some character prohibited by Windows (although I fixed that previously) in the file name.

Best,
-E

[egeulgen]

I just added a (hopeful) fix, limiting the file name to 100 characters. Let me know if this does not fix the issue and I'll try to investigate further

[travis-m-blimkie]

Tested it this morning with the update, and it's resolved the issue for me. Thanks so much for the quick response, cheers!