Question: R: Ballgown load fails
gravatar for dec986
15 months ago by
United States
dec986200 wrote:


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/':
  /usr/lib/x86_64-linux-gnu/ version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/RCurl/libs/
Execution halted

simply removing curl and reinstalling still produces the same error (

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/
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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?

rna-seq R software error • 709 views
ADD COMMENTlink written 15 months ago by dec986200
gravatar for cpad0112
15 months ago by
cpad011212k wrote:

Try reinstalling Rcurl package and see if it gets installed proper @ dec986

ADD COMMENTlink written 15 months ago by cpad011212k

thanks @cpad0112 that solved the problem. Simply, sudo R and then install.packages('Rcurl')

ADD REPLYlink written 15 months ago by dec986200

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.

ADD REPLYlink modified 15 months ago • written 15 months ago by cpad011212k
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