Hello I am trying to go through tutorial for STRINGdb since I believe I could use this a lot for my work but I keep getting the same error over and over again
library(STRINGdb) string_db <- STRINGdb$new( version="11.5", species=9606, score_threshold=200, network_type="full", input_directory="")
data(diff_exp_example1)
example1_mapped <- string_db$map( diff_exp_example1, "gene", removeUnmappedRows = TRUE )
hits <- example1_mapped$STRING_id[1:200]
All these steps work fine for me and it goes exactly as I want looking at their tutorial but the next step does not work for me
string_db$plot_network( hits )
Error in function (type, msg, asError = TRUE) : schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
Even if I continue with their tutorial where the next line works fine
example1_mapped_pval05 <- string_db$add_diff_exp_color( subset(example1_mapped, pvalue<0.05), logFcColStr="logFC" )
But the next line of code does not. It seems like I cant interact with their server
post payload information to the STRING server
payload_id <- string_db$post_payload( example1_mapped_pval05$STRING_id, colors=example1_mapped_pval05$color )
Error in function (type, msg, asError = TRUE) : schannel: CertGetCertificateChain trust error CERT_TRUST_IS_NOT_TIME_VALID
sessionInfo() R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale: [1] LC_COLLATE=Czech_Czechia.utf8 LC_CTYPE=Czech_Czechia.utf8 LC_MONETARY=Czech_Czechia.utf8 [4] LC_NUMERIC=C LC_TIME=Czech_Czechia.utf8
time zone: Europe/Prague tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] STRINGdb_2.14.0 httr_1.4.7 curl_5.2.0
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 gplots_3.1.3.1 cli_3.6.2 rlang_1.1.3 DBI_1.2.2
[6] KernSmooth_2.23-22 png_0.1-8 proto_1.0.0 sqldf_0.4-11 gtools_3.9.5
[11] bit_4.0.5 RCurl_1.98-1.14 plyr_1.8.9 hash_2.2.6.3 chron_2.3-61
[16] caTools_1.18.2 fastmap_1.1.1 bitops_1.0-7 lifecycle_1.0.4 memoise_2.0.1
[21] compiler_4.3.2 igraph_2.0.2 RSQLite_2.3.5 blob_1.2.4 RColorBrewer_1.1-3
[26] Rcpp_1.0.12 pkgconfig_2.0.3 rstudioapi_0.15.0 R6_2.5.1 magrittr_2.0.3
[31] gsubfn_0.7 tools_4.3.2 bit64_4.0.5 plotrix_3.8-4 cachem_1.0.8
It seems that you have outdated certificates on your machine. When creating a network specify the protocol parameter: protocol='http'
This should fix the issue.
The issue is related to the R cURL library on Windows, which failed to recognize valid certificates. This isn't the first time this package is misbehaving. Starting from version 12.4.1, STRINGdb now uses the
httrlibrary to handle web requests, which resolves the certificate validation problem.The 12.4.1 bugfix is pushed to bionc and should be available in the next few days. Please update your STRINGdb package in the next few days if you are experiencing the issue.
For now what worked for me was downloading the latest ca-bundle.crt certificate from https://curl.se/docs/caextract.html I had to rename the cacert.pem file and copy it into my user/AppData/Local/R/win-library/4.3/RCurl/etc That fixed the issue for me.
Thanks for the update Pavel!
Sorry for the slow response. I don't have a Windows machine, and could not reproduce the issue.
As I said it's not the first time this library caused an issue, but usually it was contained to a specific user having outdated certificates. Now it seems all STRINGdb stopped working on many (all?) Windows machines, so it needs to be fixed at the root.
Thanks Pavel! I had the same issue, and this worked for me.