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lawremi
libcurl function error when calling ucscGenomes()
Error persists even after suggestions given in issue #91
> ucscGenomes()
Error in names(df) <- names : attempt to set an attribute on NULL
In addition: Warning message:
In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x555578576270): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
Session info
> BiocManager::version()
[1] ‘3.18’
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.7 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /usr/local/intel/2022.1.2.146/mkl/2022.0.2/lib/intel64/libmkl_rt.so.2; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] 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
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.62.0 GenomicRanges_1.54.0 GenomeInfoDb_1.38.0 IRanges_2.36.0 S4Vectors_0.40.0
[6] BiocGenerics_0.48.0
I think you might need to update your libcurl to at least 7.66.0, see: https://curl.se/libcurl/c/CURLOPT_SSL_VERIFYHOST.html.
I am guessing that RCurl is setting this option to 1 by default, when it should set it to 2. This only affects older versions of libcurl though, so it may not be worth addressing. Hopefully updating helps.
Update - I tried updating RCurl to the latest version (RCurl_1.98-1.13 ), but that didn't work. I don't have system permissions to update libcurl so I wasn't able to test that yet. I saw that GenomicRanges_1.54.1 and BiocGenerics_0.48.1 updated versions, but neither changed any of my errors.