Error in file(con, "wb") : cannot open the connection

[chriswasd]

Hi

Describe the bug Currently running pathfindR v. 1.5.0.9007 with Reactome as my gene set. Function visualize_terms will generate the first 76 term diagrams then always errors out at "CDT1 association with the CDC6:ORC:origin complex". The error appears as: "Error in file(con, "wb") : cannot open the connectionn complex
In addition: Warning message: In file(con, "wb") : cannot open file 'term_visualizations/CDT1 association with the CDC6:ORC:origin complex.png': Invalid argument"

Analyzing my data with run_pathfindR and KEGG as gene set worked great, so the issue appears to be Reactome specific.

Desktop (please complete the following information):

• OS: Windows 10

R Session Information: R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

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

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

other attached packages: [1] pathfindR_1.5.0.9007

loaded via a namespace (and not attached): [1] KEGGgraph_1.46.0 ggrepel_0.8.2 Rcpp_1.0.4.6 tidyr_1.0.2
[5] png_0.1-7 Biostrings_2.54.0 assertthat_0.2.1 digest_0.6.25
[9] foreach_1.5.0 ggforce_0.3.1 R6_2.4.1 stats4_3.6.3
[13] RSQLite_2.2.0 evaluate_0.14 highr_0.8 httr_1.4.1
[17] ggplot2_3.3.0 pillar_1.4.3 zlibbioc_1.32.0 rlang_0.4.5
[21] rstudioapi_0.11 blob_1.2.1 magick_2.3 S4Vectors_0.24.4
[25] rmarkdown_2.1 labeling_0.3 stringr_1.4.0 igraph_1.2.5
[29] RCurl_1.98-1.1 polyclip_1.10-0 bit_1.1-15.2 munsell_0.5.0
[33] compiler_3.6.3 xfun_0.13 pkgconfig_2.0.3 BiocGenerics_0.32.0 [37] htmltools_0.4.0 tidyselect_1.0.0 KEGGREST_1.26.1 tibble_3.0.1
[41] gridExtra_2.3 IRanges_2.20.2 codetools_0.2-16 graphlayouts_0.6.0
[45] XML_3.99-0.3 viridisLite_0.3.0 crayon_1.3.4 dplyr_0.8.5
[49] MASS_7.3-51.5 bitops_1.0-6 grid_3.6.3 gtable_0.3.0
[53] lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5 scales_1.1.0
[57] graph_1.64.0 stringi_1.4.6 farver_2.0.3 XVector_0.26.0
[61] viridis_0.5.1 doParallel_1.0.15 ellipsis_0.3.0 vctrs_0.2.4
[65] org.Hs.eg.db_3.10.0 iterators_1.0.12 tools_3.6.3 bit64_0.9-7
[69] Biobase_2.46.0 glue_1.4.0 tweenr_1.0.1 purrr_0.3.4
[73] yaml_2.2.1 ggraph_2.0.2 parallel_3.6.3 AnnotationDbi_1.48.0 [77] colorspace_1.4-1 tidygraph_1.1.2 memoise_1.1.0 knitr_1.28

[egeulgen]

I just tried a fix. Do you mind installing the development via devtools:

devtools::install_github("egeulgen/pathfindR")

[chriswasd]

Thanks for the quick response. I installed the development version. It got a little further with 78 diagrams but has a new error: "Error in file(con, "wb") : cannot open the connection
In addition: Warning message: In file(con, "wb") : cannot open file 'term_visualizations/NIK-->noncanonical_NF-kB_signaling.png': Invalid argument"

[egeulgen]

The issue is that certain characters are not allowed for file naming on Windows. Tried another fix, should do the trick

[chriswasd]

It worked! Thanks for quickly solving the issue. pathfindR is a brilliant package!