Reactome GMT file example do not exist

[nicolau]

Hi @iza-mcac and @luciorq ,

The Isoformic is amazing, and I'm starting to use it. I have many ideas to improve the package but I'm trying to understand what I need first, executing the all commands.

I found an error:

Error: File(s) 'C:/Users/Andre.Nicolau/Documents/Programs/R/R-4.1.2/library/isoformic/extdata/c2.cp.reactome.v2023.1.Hs.symbols.gmt.txt' do not exist

When I tried this code chunk:

path_package("isoformic", "extdata", "c2.cp.reactome.v2023.1.Hs.symbols.gmt.txt")

genesets_list <- fgsea::gmtPathways(
  gmt.file = path_package("isoformic", "extdata", "c2.cp.reactome.v2023.1.Hs.symbols.gmt.txt")
)

head(str(genesets_list))
head(genesets_list[[1]])

I hope to contribute more to the Isoformic package improvement. You will see more of my messages haha...

[iza-mcac]

Hello, @nicolau I added that gmt on the package data files last afternoon! so if you update the package this error should be fixed.
Thanks a lot for pointing it out

[luciorq]

Hi @nicolau,

Thank you for your valuable input. We appreciate your feedback.

Currently, the package is in an experimental stage as we are actively working on stabilizing the API we intend to offer. Developing in the open has advantages and challenges, and your issue brings attention to an important aspect.

The specific issue you mentioned arose when we replaced a GMT file used in previous examples with a more meaningful one.

Thank you for pointing it out. We will be updating the documentation and addressing this issue soon.
Once again, any additional comments and contributions are welcome!

Best,

[nicolau]

Thank you both,

I updated the installed package, and it worked perfectly. But when I executed:

enrichment_df <- run_enrichment(
  det_df = PE1_DETs_final,
  genesets_list = genesets_list,
  pval_cutoff = 0.05
)

I found this error:

Error in `map()`:
i In index: 1.
Caused by error in `serialize()`:
! error writing to connection
Backtrace:
  1. isoformic::run_enrichment(...)
  2. purrr::map_dfr(...)
  3. purrr::map(.x, .f, ...)
  4. purrr:::map_("list", .x, .f, ..., .progress = .progress)
  8. isoformic (local) .f(.x[[i]], ...)
     ...
 18. BiocParallel:::bploop.lapply(...)
 20. BiocParallel:::bploop.iterate(...)
 22. BiocParallel::.send_to(cl, i, value_)
 24. parallel:::sendData.SOCKnode(backend[[node]], value)
 25. base::serialize(data, node$con)

By the way, I'm sending my SessionInfo():

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    
system code page: 65001

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

other attached packages:
[1] ggplot2_3.4.2        stringr_1.5.0        tidyr_1.3.0          dplyr_1.1.2          readr_2.1.4          fs_1.5.2            
[7] isoformic_0.0.0.9003

loaded via a namespace (and not attached):
 [1] viridis_0.6.3       bit64_4.0.5         vroom_1.6.3         viridisLite_0.4.2   carData_3.0-5       yaml_2.3.7         
 [7] remotes_2.4.2       ggrepel_0.9.3       pillar_1.9.0        backports_1.4.1     lattice_0.21-8      glue_1.6.2         
[13] digest_0.6.31       ggsignif_0.6.4      colorspace_2.1-0    htmltools_0.5.4     Matrix_1.5-4        pkgconfig_2.0.3    
[19] broom_1.0.5         purrr_1.0.1         scales_1.2.1        snow_0.4-4          processx_3.8.0      tzdb_0.4.0         
[25] BiocParallel_1.28.3 tibble_3.2.1        generics_0.1.3      farver_2.1.1        car_3.1-2           ggpubr_0.6.0       
[31] withr_2.5.0         cli_3.5.0           magrittr_2.0.3      crayon_1.5.2        evaluate_0.21       ps_1.7.2           
[37] fansi_1.0.4         rstatix_0.7.2       forcats_1.0.0       pkgbuild_1.4.1      tools_4.1.2         data.table_1.14.8  
[43] prettyunits_1.1.1   hms_1.1.3           lifecycle_1.0.3     munsell_0.5.0       callr_3.7.3         compiler_4.1.2     
[49] rlang_1.1.0         grid_4.1.2          rstudioapi_0.14     labeling_0.4.2      rmarkdown_2.22      gtable_0.3.3       
[55] abind_1.4-5         curl_5.0.0          R6_2.5.1            gridExtra_2.3       knitr_1.43          fastmap_1.1.0      
[61] bit_4.0.5           utf8_1.2.3          fastmatch_1.1-3     fgsea_1.20.0        rprojroot_2.0.3     desc_1.4.2         
[67] stringi_1.7.12      parallel_4.1.2      Rcpp_1.0.9          vctrs_0.6.2         tidyselect_1.2.0    xfun_0.39