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


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

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

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/ undefined symbol: PC"

How can I point R to "/opt/anaconda3/lib/" 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/': 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)

 [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     

other attached packages:
[1] BiocInstaller_1.24.0

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

> traceback()
No traceback available

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

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