Running pathfindR generates an error message in file(con, "wb")

[elouiseek]

Hi

I was hoping that you could please help. I am encountering errors when running run_pathfindR for Reactome and Go.All.

My session info:
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_South Africa.1252 LC_CTYPE=English_South Africa.1252 LC_MONETARY=English_South Africa.1252 LC_NUMERIC=C
[5] LC_TIME=English_South Africa.1252

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

other attached packages:
[1] pathfindR_1.6.1.9003 pathfindR.data_1.1.1 devtools_2.4.1 usethis_2.0.1

loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.0 bit64_4.0.5 httr_1.4.2 doParallel_1.0.16 rprojroot_2.0.2 tools_4.0.3
[8] utf8_1.2.1 R6_2.5.0 DBI_1.1.1 BiocGenerics_0.36.1 colorspace_2.0-1 withr_2.4.2 tidyselect_1.1.1
[15] gridExtra_2.3 prettyunits_1.1.1 processx_3.5.2 bit_4.0.4 curl_4.3.1 compiler_4.0.3 graph_1.68.0
[22] cli_2.5.0 Biobase_2.50.0 desc_1.3.0 labeling_0.4.2 KEGGgraph_1.50.0 scales_1.1.1 callr_3.7.0
[29] stringr_1.4.0 digest_0.6.27 rmarkdown_2.7 XVector_0.30.0 pkgconfig_2.0.3 htmltools_0.5.1.1 sessioninfo_1.1.1
[36] highr_0.9 fastmap_1.1.0 rlang_0.4.11 rstudioapi_0.13 RSQLite_2.2.7 farver_2.1.0 generics_0.1.0
[43] dplyr_1.0.6 RCurl_1.98-1.3 magrittr_2.0.1 Rcpp_1.0.6 munsell_0.5.0 S4Vectors_0.28.1 fansi_0.4.2
[50] viridis_0.6.0 lifecycle_1.0.0 yaml_2.2.1 stringi_1.5.3 ggraph_2.0.5 zlibbioc_1.36.0 MASS_7.3-53
[57] org.Hs.eg.db_3.12.0 pkgbuild_1.2.0 grid_4.0.3 blob_1.2.1 parallel_4.0.3 ggrepel_0.9.1 crayon_1.4.1
[64] Biostrings_2.58.0 graphlayouts_0.7.1 KEGGREST_1.30.1 magick_2.7.2 knitr_1.33 ps_1.6.0 pillar_1.6.0
[71] igraph_1.2.6 pak_0.1.2.1 codetools_0.2-16 stats4_4.0.3 pkgload_1.2.1 XML_3.99-0.6 glue_1.4.2
[78] evaluate_0.14 remotes_2.3.0 png_0.1-7 vctrs_0.3.8 tweenr_1.0.2 foreach_1.5.1 testthat_3.0.2
[85] gtable_0.3.0 purrr_0.3.4 polyclip_1.10-0 tidyr_1.1.3 cachem_1.0.4 ggplot2_3.3.3 xfun_0.22
[92] ggforce_0.3.3 tidygraph_1.2.0 viridisLite_0.4.0 tibble_3.1.1 iterators_1.0.13 AnnotationDbi_1.52.0 memoise_2.0.0
[99] IRanges_2.24.1 ellipsis_0.3.2

The console output for running Reactome:
run_pathfindR(Gene.df.pathfind,

•                               gene_sets = "Reactome",
  

•                               min_gset_size = 5,
  

•                               max_gset_size = 300,
  

•                               #adj_method = "fdr",
  

•                               #enrichment_threshold = 0.1 ? perhaps set to 0.1 instead of default 0.05
  

•                               output_dir = output.dir)
  

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: 13205
Number of genes in input after p-value filtering: 5936
pathfindR cannot handle p values < 1e-13. These were changed to 1e-13
Could not find any interactions for 1278 (21.53%) genes in the PIN
Final number of genes in input: 4653

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 connectionrepeat containing receptor (NLR) signaling pathways

The console output for GO:
run_pathfindR(Gene.df.pathfind,

•                        gene_sets = "GO-All",
  

•                        min_gset_size = 5,
  

•                        max_gset_size = 300,
  

•                        #adj_method = "fdr",
  

•                        #enrichment_threshold = 0.1 ? perhaps set to 0.1 instead of default 0.05
  

•                        output_dir = output.dir)
  

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: 13205
Number of genes in input after p-value filtering: 5936
pathfindR cannot handle p values < 1e-13. These were changed to 1e-13
Could not find any interactions for 1278 (21.53%) genes in the PIN
Final number of genes in input: 4653

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 connectionymerase II promoter in response to hypoxia

Thank you for your assistance!

[elouiseek]

Apologies- it is my first post and the layout did not come out as intended ;/

[egeulgen]

hey @elouiseek,

Do you mind sharing your input data frame (Gene.df.pathfind) as an RDS file so that I can look into this issue?

[ozanozisik]

May it be a path issue? Contained characters or path length?

[egeulgen]

@ozanozisik seems to be a path issue, yes. I thought I fixed that but might have missed something in visualize_term_interactions()

[elouiseek]

Sure. Thank you. I've attached the list:
Pathfinder.Gene.List.zip

[egeulgen]

thanks. I can't replicate the issue (I'm assuming since I'm on macOS and you're on Windows).

• do you have any png files in the "term_visualizations" folder under the output directory?
• do you have write permissions under the output directory?
• do you mind running the commands below (running pathfindR without visualizing the term plots and then visualizing separately)? share the error from the second command.

 res_df <- run_pathfindR(input_df,
                        gene_sets = "GO-All",
                        min_gset_size = 5,
                        max_gset_size = 300,
                        output_dir = output_dir,
                        visualize_enriched_terms = FALSE)

pin_path <- return_pin_path()
visualize_term_interactions(result_df = res_df, pin_name_path = pin_path)

• if you're comfortable with debugging in R, debugonce(visualize_term_interactions) and run the last command

[elouiseek]

Hi
-Yes, it is probably because I am on Windows.

• Yes there are some png files.
  -Yes, I have permissions.
• When I ran the two codes separately there was no errors. However, the second code did not generate output files which need to be saved in a folder. I suspect that once it runs together and generates output that it will give an error. There might still some terms which are either too long or contains symbols windows is not happy with in the Go and Reactome terms?
• I've rerun: run_pathfindR(Gene.df.pathfind,
  gene_sets = "GO-All",
  min_gset_size = 5,
  max_gset_size = 300,
  output_dir = output.dir)
  And then get the error again. The term name does look very long.
  In file(con, "wb") :
  cannot open file 'term_visualizations/DNA_damage_response,_signal_transduction_by_p53_class_mediator_resulting_in_cell_cycle_arrest.png': No such file or directory.

[elouiseek]

Thank you for the help! ;)

[egeulgen]

hello again @elouiseek,

• the second part should have generated "term_visualizations" under the current working directory, sorry I missed that
  if you run:

setwd(output_dir)
pin_path <- return_pin_path()
visualize_term_interactions(result_df = res_df, pin_name_path = pin_path)

this should save the visualizations under the output_dir

• I suspect that the "," character might be causing an issue, I've added that as a forbidden character. Could you give it a try after updating to 1.6.1.9004?

devtools::install_github("egeulgen/pathfindR")

[elouiseek]

Hi
I downloaded the latest version but it gave a similar error as well as an error with another error with a new term.
Error in file(con, "wb") : cannot open the connectionxogenous peptide antigen via MHC class I, TAP-dependent
In file(con, "wb") :
cannot open file 'term_visualizations/antigen_processing_and_presentation_of_exogenous_peptide_antigen_via_MHC_class_I__TAP-dependent.png': No such file or directory
Could file length be an issue? My output directory is also quite long, so in addition to a long term output, it might result in an error.
Thank you so much.

[egeulgen]

I've shortened the description limit to 50 characters. The output directory name should not effect. Can you give it another try using 1.6.1.9005?

[elouiseek]

Thank you so much. I reran the code with the latest update 1.6.1.9005 and it worked. ;)