Question: failed ToPASeq / igraph installation: file present, but not found
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gravatar for jan.soderman
2.8 years ago by
jan.soderman0 wrote:

Hi,

As root, I have tried to install the package 'ToPASeq' (or only the dependency 'igraph') with an error telling me that "libiconv.so.2: cannot open shared object file: No such file or directory" (see below).

Using the Linux command: locate libiconv.so.2
I can see that the file exist under the following path: /opt/anaconda3/lib/libiconv.so.2

I have tried to add this path to the LD_LIBRARY_PATH variable by editing the "/usr/lib64/R/etc/ldpaths" file like this: LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}:/opt/anaconda3/lib"

This, however, introduced another error:
"/usr/lib64/R/bin/exec/R: symbol lookup error: /opt/anaconda3/lib/libreadline.so.6: undefined symbol: PC"

How can I point R to "/opt/anaconda3/lib/libiconv.so.2" without introducing other errors?

 

This is the error message generated by the installation process:
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/lib64/R/library/igraph/libs/igraph.so':
  libiconv.so.2: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/lib64/R/library/igraph’
ERROR: dependency ‘igraph’ is not available for package ‘gRbase’
* removing ‘/usr/lib64/R/library/gRbase’
ERROR: dependencies ‘igraph’, ‘gRbase’ are not available for package ‘clipper’
* removing ‘/usr/lib64/R/library/clipper’
ERROR: dependencies ‘gRbase’, ‘clipper’ are not available for package ‘ToPASeq’
* removing ‘/usr/lib64/R/library/ToPASeq’


> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

> traceback()
No traceback available


Sincerely,
Jan
____________________
Jan Söderman, Ph.D.
Associate Professor
Medical diagnostics
Region Jönköping County
SE-551 85  Jönköping
Sweden

http://www.researchgate.net/profile/Jan_Soederman/
https://se.linkedin.com/in/jan-söderman-469555b6

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by jan.soderman0
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