Closed fazeliniah closed 1 year ago
can you share the output of sessionInfo()
?
R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
[5] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[9] matrixStats_0.62.0 limma_3.52.4
loaded via a namespace (and not attached):
[1] httr_1.4.4 BiocSingular_1.12.0 tidyr_1.2.1 jsonlite_1.8.0
[5] viridisLite_0.4.1 DelayedMatrixStats_1.18.1 gprofiler2_0.2.1 shiny_1.7.2
[9] assertthat_0.2.1 dqrng_0.3.0 GenomeInfoDbData_1.2.8 yaml_2.3.5
[13] ggrepel_0.9.1 pillar_1.8.1 lattice_0.20-45 glue_1.6.2
[17] beachmat_2.12.0 digest_0.6.29 promises_1.2.0.1 XVector_0.36.0
[21] colorspace_2.0-3 cowplot_1.1.1 htmltools_0.5.3 httpuv_1.6.6
[25] Matrix_1.5-1 plyr_1.8.7 pkgconfig_2.0.3 ggcorrplot_0.1.4
[29] zlibbioc_1.42.0 purrr_0.3.4 xtable_1.8-4 scales_1.2.1
[33] ScaledMatrix_1.4.1 later_1.3.0 tzdb_0.3.0 BiocParallel_1.30.3
[37] tibble_3.1.8 generics_0.1.3 ggplot2_3.3.6 ellipsis_0.3.2
[41] lazyeval_0.2.2 cli_3.4.1 magrittr_2.0.3 mime_0.12
[45] evaluate_0.16 fansi_1.0.3 tools_4.2.1 data.table_1.14.2
[49] hms_1.1.2 EnhancedVolcano_1.14.0 lifecycle_1.0.2 stringr_1.4.1
[53] plotly_4.10.0 munsell_0.5.0 DelayedArray_0.22.0 irlba_2.3.5
[57] compiler_4.2.1 rsvd_1.0.5 rlang_1.0.6 grid_4.2.1
[61] RCurl_1.98-1.8 rstudioapi_0.14 htmlwidgets_1.5.4 crosstalk_1.2.0
[65] rmarkdown_2.16 bitops_1.0-7 gtable_0.3.1 codetools_0.2-18
[69] DBI_1.1.3 reshape2_1.4.4 PCAtools_2.8.0 R6_2.5.1
[73] knitr_1.40 dplyr_1.0.10 fastmap_1.1.0 utf8_1.2.2
[77] readr_2.1.2 stringi_1.7.8 parallel_4.2.1 Rcpp_1.0.9
[81] vctrs_0.4.1 xfun_0.33 tidyselect_1.1.2 sparseMatrixStats_1.8.0
what is the version of pathfindR you're using? can you share sessionInfo()
after loading the library?
So sorry for the mishap. I am using 1.6.4. Here is the new sessioninfo.
sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] gprofiler2_0.2.1 pcaMethods_1.88.0 bpca_1.3-4 rgl_0.110.2
[5] scatterplot3d_0.3-42 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
[9] purrr_0.3.4 readr_2.1.2 tidyr_1.2.1 tibble_3.1.8
[13] tidyverse_1.3.2 pheatmap_1.0.12 EnhancedVolcano_1.14.0 PCAtools_2.8.0
[17] ggrepel_0.9.1 plotly_4.10.0 ggcorrplot_0.1.4 corrplot_0.92
[21] cowplot_1.1.1 ggpubr_0.4.0 gridExtra_2.3 ggplot2_3.3.6
[25] magrittr_2.0.3 knitr_1.40 pathfindR_1.6.4 pathfindR.data_1.1.2
[29] SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
[33] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[37] matrixStats_0.62.0 limma_3.52.4
loaded via a namespace (and not attached):
[1] readxl_1.4.1 backports_1.4.1 systemfonts_1.0.4 plyr_1.8.7
[5] igraph_1.3.5 lazyeval_0.2.2 BiocParallel_1.30.3 crosstalk_1.2.0
[9] digest_0.6.29 foreach_1.5.2 htmltools_0.5.3 magick_2.7.3
[13] viridis_0.6.2 fansi_1.0.3 memoise_2.0.1 ScaledMatrix_1.4.1
[17] googlesheets4_1.0.1 doParallel_1.0.17 tzdb_0.3.0 Biostrings_2.64.1
[21] graphlayouts_0.8.1 modelr_0.1.9 vroom_1.5.7 colorspace_2.0-3
[25] blob_1.2.3 rvest_1.0.3 textshaping_0.3.6 haven_2.5.1
[29] xfun_0.33 crayon_1.5.2 RCurl_1.98-1.8 jsonlite_1.8.0
[33] iterators_1.0.14 glue_1.6.2 polyclip_1.10-0 gtable_0.3.1
[37] gargle_1.2.1 zlibbioc_1.42.0 XVector_0.36.0 DelayedArray_0.22.0
[41] car_3.1-0 BiocSingular_1.12.0 abind_1.4-5 scales_1.2.1
[45] DBI_1.1.3 rstatix_0.7.0 Rcpp_1.0.9 viridisLite_0.4.1
[49] xtable_1.8-4 dqrng_0.3.0 bit_4.0.4 rsvd_1.0.5
[53] htmlwidgets_1.5.4 httr_1.4.4 RColorBrewer_1.1-3 ellipsis_0.3.2
[57] pkgconfig_2.0.3 farver_2.1.1 sass_0.4.2 dbplyr_2.2.1
[61] utf8_1.2.2 AnnotationDbi_1.58.0 labeling_0.4.2 tidyselect_1.1.2
[65] rlang_1.0.6 reshape2_1.4.4 later_1.3.0 cachem_1.0.6
[69] munsell_0.5.0 cellranger_1.1.0 tools_4.2.1 cli_3.4.1
[73] RSQLite_2.2.17 generics_0.1.3 broom_1.0.1 evaluate_0.16
[77] fastmap_1.1.0 ragg_1.2.2 yaml_2.3.5 org.Hs.eg.db_3.15.0
[81] bit64_4.0.5 fs_1.5.2 tidygraph_1.2.2 KEGGREST_1.36.3
[85] ggraph_2.0.6 sparseMatrixStats_1.8.0 mime_0.12 xml2_1.3.3
[89] compiler_4.2.1 rstudioapi_0.14 png_0.1-7 ggsignif_0.6.3
[93] reprex_2.0.2 tweenr_2.0.2 bslib_0.4.0 stringi_1.7.8
[97] highr_0.9 lattice_0.20-45 Matrix_1.5-1 vctrs_0.4.1
[101] pillar_1.8.1 lifecycle_1.0.2 jquerylib_0.1.4 data.table_1.14.2
[105] bitops_1.0-7 irlba_2.3.5 httpuv_1.6.6 R6_2.5.1
[109] promises_1.2.0.1 codetools_0.2-18 MASS_7.3-57 assertthat_0.2.1
[113] withr_2.5.0 GenomeInfoDbData_1.2.8 parallel_4.2.1 hms_1.1.2
[117] grid_4.2.1 beachmat_2.12.0 rmarkdown_2.16 DelayedMatrixStats_1.18.1
[121] carData_3.0-5 googledrive_2.0.0 ggforce_0.3.4 base64enc_0.1-3
[125] shiny_1.7.2 lubridate_1.8.0
This is odd. Can you share the command you're using and the entire console output?
I am using a very generic command for PathfindR. It works smoothly with older version of R. Here is the script:
genes_of_interest_pathfindr <- stats_df %>%dplyr::filter(adj.P.Val < 0.05 ,abs(logFC) > 0.5) %>% dplyr::select(Gene,logFC,adj.P.Val)
output_df <- run_pathfindR(genes_of_interest_pathfindr, plot_enrichment_chart = FALSE)
term_gene_heatmap <- term_gene_heatmap(output_df, use_description = TRUE) + theme(axis.text=element_text(size=5)) enrich_chart <- enrichment_chart(output_df)
pathfindR_plots <- plot_grid(enrich_chart, term_gene_heatmap, align = "v", nrow = 2, rel_heights = c(1, 1/3))
pathfindR_plots
I'm assuming you're getting the error during run_pathfindR()
can you share the entire console output for that command?
run_pathfindR(genes_of_interest_pathfindr, plot_enrichment_chart = FALSE)
n_processes
is set toiterations
becauseiterations
<n_processes
There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(9)" not to overwrite any previous results.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: 414 Number of genes in input after p-value filtering: 414 Could not find any interactions for 10 (2.42%) genes in the PIN Final number of genes in input: 404
Performing Active Subnetwork Search and Enrichment
Processing the enrichment results over all iterations
Annotating involved genes and visualizing enriched terms
Downloading pathway diagrams of 10 KEGG pathways
| | 0%Cannot download KGML file for: hsa03008 Here's the original error message: there is no package called ‘KEGGgraph’ |=========== | 10%Cannot download KGML file for: hsa04914 Here's the original error message: there is no package called ‘KEGGgraph’ |====================== | 20%Cannot download KGML file for: hsa03420 Here's the original error message: there is no package called ‘KEGGgraph’ |================================= | 30%Cannot download KGML file for: hsa03440 Here's the original error message: there is no package called ‘KEGGgraph’ |============================================ | 40%Cannot download KGML file for: hsa03030 Here's the original error message: there is no package called ‘KEGGgraph’ |======================================================== | 50%Cannot download KGML file for: hsa03430 Here's the original error message: there is no package called ‘KEGGgraph’ |=================================================================== | 60%Cannot download KGML file for: hsa05203 Here's the original error message: there is no package called ‘KEGGgraph’ |============================================================================== | 70%Cannot download KGML file for: hsa03460 Here's the original error message: there is no package called ‘KEGGgraph’ |========================================================================================= | 80%Cannot download KGML file for: hsa04217 Here's the original error message: there is no package called ‘KEGGgraph’ |==================================================================================================== | 90%Cannot download KGML file for: hsa04114 Here's the original error message: there is no package called ‘KEGGgraph’ |===============================================================================================================| 100% Saving colored pathway diagrams of 0 KEGG pathways
By default, the top 10 KEGG pathways are visualized
Please use visualize_terms()
if you'd like to plot all enriched pathways
processing file: results.Rmd |..................................... | 33% inline R code fragments
Quitting from lines 2-6 (results.Rmd) Error in knitr::include_graphics(logo_path) : Cannot find the file(s): "../extdata/logo.png"
What is the output of system.file("extdata", "logo.png", package = "pathfindR")
? It should be the path for the logo, but it seems that it somehow is returned as "../extdata/logo.png" on your system
That's right. Not sure how to fix that :(
system.file("extdata", "logo.png", package = "pathfindR") [1] "C:/Users/fazeliniah/AppData/Local/R/win-library/4.2/pathfindR/extdata/logo.png"
are you sure you have write permission under the current working directory?
I started the Rstudio in "Run as Admin" mode and still get the same error. For now, I am switching back to R-4.1.2. It works with no issues.
Thank you so much for developing this great tool. I have been using pathfindR for few weeks now. It was working smoothly on R-4.1.2. I have recently updated the R to R-4.2.1 and am getting a new error. Can you please look into this?
Downloading pathway diagrams of 10 KEGG pathways
|=====================================================================================================| 100% Saving colored pathway diagrams of 0 KEGG pathways
|.................................. | 33% inline R code fragments
Error in knitr::include_graphics(logo_path) : Cannot find the file(s): "../extdata/logo.png"