kyle-kroll
commented
1 year ago Today I updated R to 4.3.1 and reinstalled pathfindR using BiocManager and this issue was resolved with no changes to the code. Below is the new sessionInfo()
sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3.1
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] pathfindR_2.1.0 pathfindR.data_2.0.0 ggrepel_0.9.3
[4] tidyr_1.3.0 dplyr_1.1.2 ggplot2_3.4.2
[7] clusterProfiler_4.9.0.002loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 jsonlite_1.8.5 rstudioapi_0.14
[4] magrittr_2.0.3 magick_2.7.4 rmarkdown_2.22
[7] farver_2.1.1 fs_1.6.2 zlibbioc_1.46.0
[10] vctrs_0.6.3 memoise_2.0.1 RCurl_1.98-1.12
[13] ggtree_3.8.0 htmltools_0.5.5 usethis_2.2.1
[16] curl_5.0.1 gridGraphics_0.5-1 htmlwidgets_1.6.2
[19] desc_1.4.2 plyr_1.8.8 cachem_1.0.8
[22] igraph_1.5.0 iterators_1.0.14 mime_0.12
[25] lifecycle_1.0.3 pkgconfig_2.0.3 gson_0.1.0
[28] Matrix_1.5-4.1 R6_2.5.1 fastmap_1.1.1
[31] GenomeInfoDbData_1.2.10 shiny_1.7.4 digest_0.6.32
[34] aplot_0.1.10 enrichplot_1.20.0 colorspace_2.1-0
[37] patchwork_1.1.2 AnnotationDbi_1.62.1 S4Vectors_0.38.1
[40] ps_1.7.5 rprojroot_2.0.3 pkgload_1.3.2
[43] RSQLite_2.3.1 org.Hs.eg.db_3.17.0 labeling_0.4.2
[46] fansi_1.0.4 httr_1.4.6 polyclip_1.10-4
[49] compiler_4.3.1 remotes_2.4.2 doParallel_1.0.17
[52] bit64_4.0.5 withr_2.5.0 downloader_0.4
[55] BiocParallel_1.34.2 viridis_0.6.3 DBI_1.1.3
[58] pkgbuild_1.4.2 ggforce_0.4.1 MASS_7.3-60
[61] sessioninfo_1.2.2 HDO.db_0.99.1 tools_4.3.1
[64] scatterpie_0.2.1 ape_5.7-1 httpuv_1.6.11
[67] glue_1.6.2 callr_3.7.3 nlme_3.1-162
[70] GOSemSim_2.26.0 promises_1.2.0.1 shadowtext_0.1.2
[73] grid_4.3.1 reshape2_1.4.4 fgsea_1.26.0
[76] generics_0.1.3 gtable_0.3.3 data.table_1.14.8
[79] tidygraph_1.2.3 utf8_1.2.3 XVector_0.40.0
[82] BiocGenerics_0.46.0 foreach_1.5.2 pillar_1.9.0
[85] stringr_1.5.0 yulab.utils_0.0.6 later_1.3.1
[88] splines_4.3.1 tweenr_2.0.2 treeio_1.24.1
[91] lattice_0.21-8 bit_4.0.5 tidyselect_1.2.0
[94] GO.db_3.17.0 Biostrings_2.68.1 miniUI_0.1.1.1
[97] knitr_1.43 gridExtra_2.3 IRanges_2.34.1
[100] xfun_0.39 stats4_4.3.1 graphlayouts_1.0.0
[103] Biobase_2.60.0 devtools_2.4.5 KEGGgraph_1.60.0
[106] stringi_1.7.12 lazyeval_0.2.2 ggfun_0.1.1
[109] evaluate_0.21 codetools_0.2-19 ggraph_2.1.0
[112] tibble_3.2.1 qvalue_2.32.0 Rgraphviz_2.44.0
[115] graph_1.78.0 BiocManager_1.30.21 ggplotify_0.1.1
[118] cli_3.6.1 xtable_1.8-4 munsell_0.5.0
[121] processx_3.8.1 Rcpp_1.0.10 GenomeInfoDb_1.36.1
[124] png_0.1-8 XML_3.99-0.14 parallel_4.3.1
[127] ellipsis_0.3.2 blob_1.2.4 prettyunits_1.1.1
[130] profvis_0.3.8 DOSE_3.27.1 urlchecker_1.0.1
[133] bitops_1.0-7 viridisLite_0.4.2 tidytree_0.4.2
[136] scales_1.2.1 purrr_1.0.1 crayon_1.5.2
[139] rlang_1.1.1 cowplot_1.1.1 fastmatch_1.1-3
[142] KEGGREST_1.40.0
Describe the bug Running the
visualize_terms()function never completes due to issues downloading KEGG pathways.To Reproduce Steps to reproduce the behavior: Here is an example of the data frame I am using for input:
I then run the following commands:
output_df <- run_pathfindR(pathway.df, pin_name_path = "KEGG")input_processed <- input_processing(pathway.df)visualize_terms( result_df = output_df, input_processed = input_processed, hsa_KEGG = TRUE )Upon which I get the following error for all 142 KEGG pathways in the output:
Expected behavior Expected behavior is downloaded and colored KEGG pathways per the documentation.
Screenshots N/A
Desktop (please complete the following information):
R Session Information:
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] pathfindR_2.1.0.9000 pathfindR.data_2.0.0
loaded via a namespace (and not attached): [1] Biobase_2.54.0 viridis_0.6.2 httr_1.4.3
[4] tidyr_1.3.0 tidygraph_1.2.0 bit64_4.0.5
[7] viridisLite_0.4.1 foreach_1.5.2 ggraph_2.0.5
[10] stats4_4.1.2 blob_1.2.3 GenomeInfoDbData_1.2.7 [13] ggrepel_0.9.2 pillar_1.8.1 RSQLite_2.2.15
[16] glue_1.6.2 digest_0.6.31 XVector_0.34.0
[19] polyclip_1.10-0 colorspace_2.1-0 htmltools_0.5.3
[22] XML_3.99-0.8 pkgconfig_2.0.3 zlibbioc_1.40.0
[25] purrr_1.0.1 scales_1.2.1 tweenr_1.0.2
[28] ggforce_0.3.3 tibble_3.1.8 KEGGREST_1.34.0
[31] generics_0.1.3 farver_2.1.1 IRanges_2.28.0
[34] ggplot2_3.4.1 cachem_1.0.6 withr_2.5.0
[37] BiocGenerics_0.40.0 cli_3.6.0 magrittr_2.0.3
[40] crayon_1.5.2 memoise_2.0.1 evaluate_0.20
[43] KEGGgraph_1.54.0 fansi_1.0.4 doParallel_1.0.17
[46] MASS_7.3-55 graph_1.72.0 tools_4.1.2
[49] org.Hs.eg.db_3.14.0 lifecycle_1.0.3 S4Vectors_0.32.3
[52] munsell_0.5.0 AnnotationDbi_1.56.2 Biostrings_2.62.0
[55] compiler_4.1.2 GenomeInfoDb_1.30.1 rlang_1.0.6
[58] grid_4.1.2 RCurl_1.98-1.5 iterators_1.0.14
[61] rstudioapi_0.13 igraph_1.3.5 bitops_1.0-7
[64] labeling_0.4.2 rmarkdown_2.11 gtable_0.3.1
[67] codetools_0.2-18 curl_4.3.2 DBI_1.1.3
[70] graphlayouts_0.8.0 R6_2.5.1 gridExtra_2.3
[73] knitr_1.37 dplyr_1.1.0 fastmap_1.1.0
[76] bit_4.0.4 utf8_1.2.3 Rgraphviz_2.38.0
[79] parallel_4.1.2 Rcpp_1.0.10 vctrs_0.5.2
[82] png_0.1-8 tidyselect_1.2.0 xfun_0.29
Additional context I have tried downloading the most recent dev branch using the
pakpackage as well as updating magick per another issue thread from a few years ago. I know this is NOT internet related since I've tried it on both wifi and wired gigabit internet that has no issues connecting to the KEGG API or websites. For example using the KEGG API to callhttps://rest.kegg.jp/get/hsa05202/imageresults in the correct pathway being immediately downloaded.