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rcurlubuntu-20.04biomart

CURL_OPENSSL_3 problem while installing biomaRt R package on Ubuntu 20.04

Problem

I am trying to install biomaRt R package, but I have been experiencing problems. I have also noticed that the same problem also occurs with some other packages like twitteR. It seems like it is a problem related to curl.

When I run the following installation command below:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")

I receive the following error message:

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'biomaRt'
also installing the dependency ‘BiocFileCache’

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocFileCache_1.10.2.tar.gz'
Content type 'application/x-gzip' length 288347 bytes (281 KB)
==================================================
downloaded 281 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/biomaRt_2.42.1.tar.gz'
Content type 'application/x-gzip' length 431995 bytes (421 KB)
==================================================
downloaded 421 KB

* installing *source* package ‘BiocFileCache’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/local/lib/R/site-library/curl/libs/curl.so':
  /usr/local/lib/R/site-library/curl/libs/curl.so: undefined symbol: curl_easy_strerror, version CURL_OPENSSL_3
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

Question

Have you experienced something similar? If so, how did you solve it?

Attempts to solve

  1. Tried to install RCurl package as mentioned here, but it did not help.

  2. Tried installing libcurl3 as mentioned here. However, it breaks down R installation.

  3. Tried re-installing R.

And none of above worked for me.

R session info

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] crayon_1.3.4        dplyr_1.0.2         grid_3.6.3          R6_2.4.1            gtable_0.3.0        lifecycle_0.2.0    
 [7] magrittr_1.5        scales_1.1.1        ggplot2_3.3.2       pillar_1.4.6        rlang_0.4.7         rstudioapi_0.11    
[13] vctrs_0.3.4         generics_0.0.2      ellipsis_0.3.1      tools_3.6.3         glue_1.4.2          munsell_0.5.0      
[19] purrr_0.3.4         compiler_3.6.3      colorspace_1.4-1    pkgconfig_2.0.3     BiocManager_1.30.10 tidyselect_1.1.0   
[25] tibble_3.0.3
Solution

  • While I was writing this thread, I came across a simple solution.

    Basically uninstalling and installing R curl package helped.

    remove.packages("curl")
install.packages("curl")