R: Ballgown load fails
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0
Entering edit mode
3.3 years ago
dec986 ▴ 310

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 • 1.5k views
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Entering edit mode
3.3 years ago

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

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Entering edit mode

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

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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.

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