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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Fail downloading png file from KEGG #127

Closed powerhorse1986 closed 2 years ago

powerhorse1986 commented 2 years ago

Describe the bug 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument

To Reproduce Steps to reproduce the behavior:

  1. Executing run_pathfindR(input_df, max_to_plot = 25)

Expected behavior The top 25 enriched terms supposed to be downloaded and colored.

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

R Session Information: R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] WGCNA_1.71 fastcluster_1.2.3 dynamicTreeCut_1.63-1 writexl_1.4.0 magrittr_2.0.3 pathfindR_1.6.3
[7] pathfindR.data_1.1.2 org.Hs.eg.db_3.15.0 rtracklayer_1.56.0 fdrtool_1.2.17 gprofiler2_0.2.1 gProfileR_0.7.0
[13] edgeR_3.38.1 limma_3.52.1 kohonen_3.0.11 gridExtra_2.3 gridGraphics_0.5-1 RCircos_1.2.2
[19] DT_0.23 formattable_0.2.1 GetoptLong_1.0.5 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
[25] tidyr_1.2.0 tibble_3.1.7 tidyverse_1.3.1 GenomicFeatures_1.48.1 AnnotationDbi_1.58.0 rhdf5_2.40.0
[31] ggvenn_0.1.9 dplyr_1.0.9 hash_2.2.6.2 ggplotify_0.1.0 png_0.1-7 reactable_0.3.0
[37] htmltools_0.5.2 RSQLite_2.2.14 kableExtra_1.3.4 psych_2.2.5 reshape2_1.4.4 GGally_2.1.2
[43] biomaRt_2.52.0 gplots_3.1.3 ggplot2_3.3.6 PoiClaClu_1.0.2.1 RColorBrewer_1.1-3 pheatmap_1.0.12
[49] DESeq2_1.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.0 matrixStats_0.62.0 GenomicRanges_1.48.0
[55] GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 tximport_1.24.0 readr_2.1.2
[61] knitr_1.39

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 prabclus_2.3-2 R.methodsS3_1.8.2 bit64_4.0.5 irlba_2.3.5 DelayedArray_0.22.0
[7] R.utils_2.11.0 rpart_4.1.16 data.table_1.14.2 KEGGREST_1.36.0 RCurl_1.98-1.7 doParallel_1.0.17
[13] generics_0.1.2 preprocessCore_1.58.0 bit_4.0.4 tzdb_0.3.0 webshot_0.5.3 xml2_1.3.3
[19] lubridate_1.8.0 assertthat_0.2.1 viridis_0.6.2 xfun_0.31 hms_1.1.1 jquerylib_0.1.4
[25] evaluate_0.15 DEoptimR_1.0-11 fansi_1.0.3 restfulr_0.0.15 progress_1.2.2 caTools_1.18.2
[31] dbplyr_2.2.0 readxl_1.4.0 Rgraphviz_2.40.0 igraph_1.3.2 DBI_1.1.2 geneplotter_1.74.0
[37] htmlwidgets_1.5.4 reshape_0.8.9 ellipsis_0.3.2 crosstalk_1.2.0 backports_1.4.1 annotate_1.74.0
[43] vctrs_0.4.1 cachem_1.0.6 withr_2.5.0 ggforce_0.3.3 robustbase_0.95-0 checkmate_2.1.0
[49] GenomicAlignments_1.32.0 prettyunits_1.1.1 mclust_5.4.10 mnormt_2.1.0 svglite_2.1.0 cluster_2.1.3
[55] lazyeval_0.2.2 crayon_1.5.1 genefilter_1.78.0 pkgconfig_2.0.3 labeling_0.4.2 tweenr_1.0.2
[61] nlme_3.1-158 nnet_7.3-17 rlang_1.0.2 diptest_0.76-0 lifecycle_1.0.1 filelock_1.0.2
[67] BiocFileCache_2.4.0 modelr_0.1.8 invgamma_1.1 cellranger_1.1.0 polyclip_1.10-0 graph_1.74.0
[73] Matrix_1.4-1 ashr_2.2-54 Rhdf5lib_1.18.2 base64enc_0.1-3 reprex_2.0.1 GlobalOptions_0.1.2
[79] viridisLite_0.4.0 rjson_0.2.21 bitops_1.0-7 R.oo_1.25.0 KernSmooth_2.23-20 rhdf5filters_1.8.0
[85] Biostrings_2.64.0 blob_1.2.3 shape_1.4.6 mixsqp_0.3-43 SQUAREM_2021.1 jpeg_0.1-9
[91] scales_1.2.0 memoise_2.0.1 plyr_1.8.7 zlibbioc_1.42.0 compiler_4.2.1 BiocIO_1.6.0
[97] clue_0.3-61 KEGGgraph_1.56.0 Rsamtools_2.12.0 cli_3.3.0 XVector_0.36.0 htmlTable_2.4.0
[103] Formula_1.2-4 MASS_7.3-57 tidyselect_1.1.2 stringi_1.7.6 highr_0.9 yaml_2.3.5
[109] locfit_1.5-9.5 latticeExtra_0.6-29 ggrepel_0.9.1 sass_0.4.1 tools_4.2.1 parallel_4.2.1
[115] circlize_0.4.15 rstudioapi_0.13 foreign_0.8-82 foreach_1.5.2 farver_2.1.0 ggraph_2.0.5
[121] digest_0.6.29 fpc_2.2-9 Rcpp_1.0.8.3 broom_0.8.0 httr_1.4.3 ComplexHeatmap_2.12.0
[127] kernlab_0.9-31 colorspace_2.0-3 rvest_1.0.2 XML_3.99-0.10 fs_1.5.2 truncnorm_1.0-8
[133] splines_4.2.1 yulab.utils_0.0.4 graphlayouts_0.8.0 flexmix_2.3-18 plotly_4.10.0 systemfonts_1.0.4
[139] xtable_1.8-4 jsonlite_1.8.0 tidygraph_1.2.1 modeltools_0.2-23 R6_2.5.1 Hmisc_4.7-0
[145] pillar_1.7.0 glue_1.6.2 fastmap_1.1.0 BiocParallel_1.30.2 class_7.3-20 codetools_0.2-18
[151] utf8_1.2.2 lattice_0.20-45 bslib_0.3.1 curl_4.3.2 gtools_3.9.2.2 magick_2.7.3
[157] GO.db_3.15.0 survival_3.3-1 rmarkdown_2.14 munsell_0.5.0 GenomeInfoDbData_1.2.8 iterators_1.0.14
[163] impute_1.70.0 haven_2.5.0 gtable_0.3.0

Additional context Add any other context about the problem here. While pathfindR is an R package, the active subnetwork search functionality is written in Java. If you suspect any issue regarding java please provide your Java version (by running java --version)

egeulgen commented 2 years ago

updating KEGGREST should resolve the issue

see: https://github.com/egeulgen/pathfindR/issues/121#issuecomment-1163167953