I have codes to download updated KEGG pathways that I have run thousands of times that now fail with an error. Here is a reproducible example using
> library(limma) > library(Mus.musculus) Loading required package: AnnotationDbi #... deleted for space > univ_EG <- keys(Mus.musculus, keytype = "ENTREZID") > sel_EG <- univ_EG[200:1200] > kegg_out <- kegga(sel_EG, universe = univ_EG, + species.KEGG = "mmu") Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : cannot read from connection In addition: Warning message: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : URL 'https://rest.kegg.jp/link/pathway/mmu': status was 'Failure when receiving data from the peer'
I went to KEGG and this notice was posted that KEGG API moving to HTTPS as of June 1, 2022: https://www.genome.jp/kegg/docs/announce.html . I think this may be the cause of my problem and also this recent post KEGG Pathway in R . Anyone know what settings I need to change?
sessionInfo( ) R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) Matrix products: default locale:  LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8  LC_MONETARY=English_United States.utf8  LC_NUMERIC=C  LC_TIME=English_United States.utf8 attached base packages:  stats4 stats graphics grDevices utils datasets methods  base other attached packages:  Mus.musculus_1.3.1  TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0  org.Mm.eg.db_3.15.0  GO.db_3.15.0  OrganismDbi_1.38.0  GenomicFeatures_1.48.0  GenomicRanges_1.48.0  GenomeInfoDb_1.32.1  AnnotationDbi_1.58.0  IRanges_2.30.0  S4Vectors_0.34.0  Biobase_2.56.0  BiocGenerics_0.42.0  limma_3.52.0 loaded via a namespace (and not attached):  MatrixGenerics_1.8.0 httr_1.4.3  bit64_4.0.5 assertthat_0.2.1  BiocManager_1.30.18 BiocFileCache_2.4.0  RBGL_1.72.0 blob_1.2.3  GenomeInfoDbData_1.2.8 Rsamtools_2.12.0  yaml_2.3.5 progress_1.2.2  pillar_1.7.0 RSQLite_2.2.13  lattice_0.20-45 glue_1.6.2  digest_0.6.29 XVector_0.36.0  Matrix_1.4-1 XML_3.99-0.9  pkgconfig_2.0.3 biomaRt_2.52.0  zlibbioc_1.42.0 purrr_0.3.4  BiocParallel_1.30.0 tibble_3.1.6  KEGGREST_1.36.0 generics_0.1.2  ellipsis_0.3.2 cachem_1.0.6  SummarizedExperiment_1.26.0 cli_3.3.0  magrittr_2.0.3 crayon_1.5.1  memoise_2.0.1 fansi_1.0.3  xml2_1.3.3 graph_1.74.0  tools_4.2.0 prettyunits_1.1.1  hms_1.1.1 BiocIO_1.6.0  lifecycle_1.0.1 matrixStats_0.62.0  stringr_1.4.0 DelayedArray_0.22.0  Biostrings_2.64.0 compiler_4.2.0  rlang_1.0.2 grid_4.2.0  RCurl_1.98-1.6 rstudioapi_0.13  rjson_0.2.21 rappdirs_0.3.3  bitops_1.0-7 restfulr_0.0.13  DBI_1.1.2 curl_4.3.2  R6_2.5.1 GenomicAlignments_1.32.0  dplyr_1.0.9 rtracklayer_1.56.0  fastmap_1.1.0 bit_4.0.4  utf8_1.2.2 filelock_1.0.2  stringi_1.7.6 parallel_4.2.0  Rcpp_220.127.116.11 vctrs_0.4.1  png_0.1-7 dbplyr_2.1.1  tidyselect_1.1.2