Error in download.KEGG.Path(species)

[shenshenwu5]

Hi, Prof. Yu, Thanks for your software to make it convenient for me to do analysis. But i meet some unsloved probblems and need your help. I can use R/clusterProfiler until two days ago, but it suddenly unable to use normally when do enrichKEGG.

i use the right organism name for maize, but it said can't search. And i trid 'hsa', but it work well. I google the same problem, some sad the problem is the network. And my browser showed i can open the KEGG website. So I don't known how to solve this problem, and hope you can help me to solve it.

Thanks;

[shenshenwu5]

I just used the same script as three days ago, and this problem occurred.

[shenshenwu5]

what's more, it works well with enrichGO.

[huerqiang]

@shenshen-wu This is indeed a network problem, you can close R and run again. In addition, the versions of your R and R packages (such as clusterProfiler, GO.db) are too old, I suggest you update them.

[shenshenwu5]

Thanks, it works well after three days. It seems that this problem turely because of the network. But i still hope this can be improved in the next version.

Thanks for your replay~

[gaospecial]

Thanks, it works well after three days. It seems that this problem turely because of the network. But i still hope this can be improved in the next version.

Thanks for your replay~

I have encounter such issues many times. But for the first time, I found the REST api raised a HTTP 400 error this week, and this error is only found for some of the request.

I have to say the KEGG database is unstable sometimes.

[GuangchuangYu]

should works in newest version, see https://github.com/YuLab-SMU/clusterProfiler/issues/256#issuecomment-773907348.

[mdtorohernando]

thank you for your comments, today, after reinstalling all the packages I have found a new error, it seems to be Kegg database

kk_up = enrichKEGG(gene = gene_up, organism = 'mmu', pvalueCutoff = 0.05, qvalueCutoff = 0.05, use_internal_data = F)
Reading KEGG annotation online:

fail to download KEGG data... Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... Además: Warning message: In utils::download.file(url, quiet = TRUE, method = method, ...) : URL 'http://rest.kegg.jp/link/mmu/pathway': status was 'Couldn't connect to server'

I attach my sessionInfo.

I don't know how to solve that.

Thanks

sessionInfo.annot.txt

[minglu-xie]

If you run library(clusterProfiler) getOption("clusterProfiler.download.method") You may get the answer "libcurl". Actually this may be the reason why you cannot download KEGG data. You can try this install.packages("R.utils")

library(R.utils)

R.utils::setOption("clusterProfiler.download.method","auto") Then it should work to download KEGG data. ----From teacher Jimmy

[Leandromvelez]

If you run library(clusterProfiler) getOption("clusterProfiler.download.method") You may get the answer "libcurl". Actually this may be the reason why you cannot download KEGG data. You can try this install.packages("R.utils")

library(R.utils)

R.utils::setOption("clusterProfiler.download.method","auto") Then it should work to download KEGG data. ----From teacher Jimmy

It worked for me! Thank you @ml-john and teacher Jimmy

[Guerande29]

Oh thank you. I was having this problem and I can solve reading this issue.

And I take this opportunity to ask: How can I make the graphic visualization of the KEGG for clustercompare using fun=enrichKEGG? Could you show me some command lines, especially I would like to visualize the pathway with the genes

Thanks,

[rimorob]

I'm having the same problem. I've reinstalled clusterProfiler, installed R.utils, tried setting the download method to auto, etc. No luck. R version 4.1.2. Session info output: other attached packages: [1] R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2 clusterProfiler_4.0.5

loaded via a namespace (and not attached): [1] fgsea_1.18.0 colorspace_2.0-3 ggtree_3.0.4 qvalue_2.24.0
[5] XVector_0.32.0 GenomicRanges_1.44.0 aplot_0.1.8 rstudioapi_0.14
[9] farver_2.1.1 graphlayouts_0.8.3 ggrepel_0.9.2 bit64_4.0.5
[13] AnnotationDbi_1.54.1 fansi_1.0.3 scatterpie_0.1.8 splines_4.1.2
[17] cachem_1.0.6 GOSemSim_2.18.1 geneplotter_1.70.0 polyclip_1.10-4
[21] jsonlite_1.8.3 annotate_1.70.0 GO.db_3.13.0 png_0.1-7
[25] ggforce_0.4.1 compiler_4.1.2 httr_1.4.4 assertthat_0.2.1
[29] Matrix_1.5-3 fastmap_1.1.0 lazyeval_0.2.2 cli_3.4.1
[33] tweenr_2.0.2 tools_4.1.2 igraph_1.3.5 gtable_0.3.1
[37] glue_1.6.2 GenomeInfoDbData_1.2.6 reshape2_1.4.4 DO.db_2.9
[41] dplyr_1.0.10 fastmatch_1.1-3 Rcpp_1.0.9 enrichplot_1.12.3
[45] Biobase_2.52.0 vctrs_0.5.0 Biostrings_2.60.2 ape_5.6-2
[49] nlme_3.1-155 ggraph_2.1.0 stringr_1.4.1 lifecycle_1.0.3
[53] XML_3.99-0.12 DOSE_3.18.3 zlibbioc_1.38.0 MASS_7.3-55
[57] scales_1.2.1 tidygraph_1.2.2 MatrixGenerics_1.4.3 parallel_4.1.2
[61] SummarizedExperiment_1.22.0 RColorBrewer_1.1-3 memoise_2.0.1 gridExtra_2.3
[65] ggplot2_3.4.0 downloader_0.4 ggfun_0.0.8 yulab.utils_0.0.5
[69] stringi_1.7.8 RSQLite_2.2.18 genefilter_1.74.1 S4Vectors_0.30.2
[73] tidytree_0.4.1 BiocGenerics_0.38.0 BiocParallel_1.26.2 GenomeInfoDb_1.28.4
[77] rlang_1.0.6 pkgconfig_2.0.3 bitops_1.0-7 matrixStats_0.62.0
[81] lattice_0.20-45 purrr_0.3.5 treeio_1.16.2 patchwork_1.1.2
[85] cowplot_1.1.1 shadowtext_0.1.2 bit_4.0.4 tidyselect_1.2.0
[89] plyr_1.8.8 magrittr_2.0.3 DESeq2_1.32.0 R6_2.5.1
[93] IRanges_2.26.0 generics_0.1.3 DelayedArray_0.18.0 DBI_1.1.3
[97] pillar_1.8.1 withr_2.5.0 survival_3.2-13 KEGGREST_1.32.0
[101] RCurl_1.98-1.9 tibble_3.1.8 crayon_1.5.2 utf8_1.2.2
[105] viridis_0.6.2 locfit_1.5-9.6 grid_4.1.2 data.table_1.14.4
[109] blob_1.2.3 digest_0.6.30 xtable_1.8-4 tidyr_1.2.1
[113] gridGraphics_0.5-1 stats4_4.1.2 munsell_0.5.0 viridisLite_0.4.1
[117] ggplotify_0.1.0

[rimorob]

Actually, this fixed it: R.utils::setOption("clusterProfiler.download.method","wget")

[rintukutum]

For Mac M1 users, R.utils::setOption("clusterProfiler.download.method","curl")

[lucygarner]

What is the appropriate option for CentOS Linux 7? I haven't had any success with the options above, but it was working fine two days ago, so I'm wondering if the server is actually down?