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lawremi / rtracklayer

R interface to genome annotation files and the UCSC genome browser
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libcurl function error when calling ucscGenomes() #101

Open slsevilla opened 8 months ago

slsevilla commented 8 months ago

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
lawremi commented 8 months ago

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.

slsevilla commented 8 months ago

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.

slsevilla commented 7 months ago

Hi- any other ideas or fixes here?