Entering edit mode
5.7 years ago
dec986
▴
370
Hello,
I updated my Ubuntu installation to 18.04 (support for 17.10 expired), and now I can no longer load Ballgown in R.
I get the following error:
con@con-VirtualBox:~/RNASeqb/Milanovich/genomeNext/compare$ Rscript pathfinder.ballgown.R
Loading required package: methods
Error: package or namespace load failed for ‘ballgown’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/RCurl/libs/RCurl.so':
/usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/RCurl/libs/RCurl.so)
Execution halted
simply removing curl and reinstalling still produces the same error (https://community.rstudio.com/t/error-version-curl-openssl-3-not-found/8090)
my session information:
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] 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] compiler_3.4.4
How can I get ballgown working?
thanks @cpad0112 that solved the problem. Simply,
sudo R
and theninstall.packages('Rcurl')
Though it solved the problem, user is supposed minimize the use of sudo esp for these kind of tasks where user can install packages in home/local space. You should be able set up all R libraries in your home/local directory by setting up
.Renviron
.