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
