Question: R: Ballgown load fails
0
gravatar for dec986
23 months ago by
dec986230
United States
dec986230 wrote:

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?

rna-seq R software error • 1.0k views
ADD COMMENTlink written 23 months ago by dec986230
1
gravatar for cpad0112
23 months ago by
cpad011213k
India
cpad011213k wrote:

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

ADD COMMENTlink written 23 months ago by cpad011213k

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

ADD REPLYlink written 23 months ago by dec986230
1

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 23 months ago • written 23 months ago by cpad011213k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 703 users visited in the last hour