I am experiencing an issue with the STRINGdb R package.
The code I run is:
> library("STRINGdb")
> string_db <- STRINGdb$new( version="11.5", species=9606, score_threshold=200, input_directory="")
> string_proteins <- string_db$get_proteins()
Running the last line of the code returns the following error message:
trying URL 'https://stringdb-static.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Error in download.file(urlStr, temp) :
cannot open URL 'https://stringdb-static.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
In addition: Warning message:
In download.file(urlStr, temp) :
URL 'https://stringdb-static.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz': status was 'Peer certificate cannot be authenticated with given CA certificates'
sessionInfo( )
``` R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] el_GR.UTF-8/el_GR.UTF-8/el_GR.UTF-8/C/el_GR.UTF-8/el_GR.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] STRINGdb_2.6.0
loaded via a namespace (and not attached):
[1] igraph_1.2.6 hash_2.2.6.1 Rcpp_1.0.7 magrittr_2.0.1 bit_4.0.4
[6] rlang_0.4.11 fastmap_1.1.0 blob_1.2.1 plyr_1.8.6 caTools_1.18.2
[11] tools_4.1.0 png_0.1-7 plotrix_3.8-1 KernSmooth_2.23-20 DBI_1.1.1
[16] gtools_3.9.2 bit64_4.0.5 BiocManager_1.30.16 RColorBrewer_1.1-2 vctrs_0.3.8
[21] bitops_1.0-7 RCurl_1.98-1.3 cachem_1.0.5 memoise_2.0.0 RSQLite_2.2.7
[26] gsubfn_0.7 compiler_4.1.0 gplots_3.1.1 chron_2.3-56 sqldf_0.4-11
[31] proto_1.0.0 pkgconfig_2.0.3
It seems to be an issue with certificates on OSX Mojave
There seem to be no good solution for that, sans updating to Big Sur or newer OSX. I would install STRINGdb package from source and change all occurrences of "https://stringdb-static.org" to "http://stringdb-static.org".
This should work around the certificate issue.
I changed all occurrences of "https://stringdb-static.org" to "http://stringdb-static.org". Then I installed STRINGdb package from source and it WORKED!!!
Thank you so much Damian!!!
Hi, could you please explain how did you change the occurrences after installing the package??
Thanks in advance
If you are still encountering the issue in STRINGdb version >= 2.6.1 you can now add parameter
protocol="http"when you create the STRINGdb object:This should fix the issue with the certificates.