I can’t install the stringi package on Centos

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I’m trying to install the package stringi in a cluster that rotates Centos 7, but I am failing miseravelvente. The error that occurs is below:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so':
  /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi’

The downloaded source packages are in
    ‘/tmp/RtmpHKpp7q/downloaded_packages’
Warning message:
In install.packages("stringi") :
  installation of package ‘stringi’ had non-zero exit status

I already asked this question in the original OS and got a comment on it, but my ignorance on Linux did not allow me to understand what I need to do. I know it has something to do with libstdc++.so.6, but I can go no further than this.

The details of the R where I tried to install the package are below.

> sessionInfo()
R version 3.3.1 (2016-06-21)
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

loaded via a namespace (and not attached):
[1] tools_3.3.1
r

  • Have you tried anything like this? http://stackoverflow.com/q/16620942/3297472

  • I just tried. It didn’t work. I keep getting the same error message I put to the above question, even though I ran sudo yum install libstdc++*.

  • I think this can solve: http://stackoverflow.com/a/20357035/3297472

  • No. Nothing worked out. I even installed all the packages with gcc that exist in yum, set the path of the Libraries as in this link and yet, I keep getting the same error. The funny thing is that I don’t have this problem on Ubuntu or macOS (even installing the source version of the package). Only Centos who won’t cooperate with me.

1 answer

3


I discovered the problem. When rotating

strings /usr/lib64/libstdc++.so.6 | grep CXXABI

receive the output

CXXABI_1.3
CXXABI_1.3.1
CXXABI_1.3.2
CXXABI_1.3.3
CXXABI_1.3.4
CXXABI_1.3.5
CXXABI_1.3.6
CXXABI_1.3.7
CXXABI_TM_1

I mean, I don’t have the CXXABI_1.3.8 installed in the cluster. When I went to investigate the reason for this, I discovered that it could be my version of gcc that was out of date. I went to check which version I had and bingo:

$ gcc -v
gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)

Now it was just a matter of installing the gcc 4.9.x. To do this in Centos, just rotate

$ sudo yum install devtoolset-3-gcc-c++
$ sudo yum install devtoolset-3-gcc-gfortran
$ scl enable devtoolset-3 bash

The first two commands install the C, C++ and Fortran compilers. The third one tells the operating system to use the gcc 4.9.x as standard compiler. So when I check which version of gcc is active in the cluster, I get the following:

$ gcc -v
gcc version 4.9.2 20150212 (Red Hat 4.9.2-6) (GCC)

This done, just enter the R, execute install.packages("stringi") and install the package normally.

In short, my problem was the version of gcc installed in the machine. As far as I have ascertained, the stringi requires it to be version 4.9.x. The older version 4.8.x did not work, just as 5.3.0 did not work either.

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