Centos 6.3 R installation error
i am newbie centos so i have tried to install R. It's installed but giving this error when i write console
R
Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/utils/libs/utils.so':
/usr/lib64/R/library/utils/libs/utils.so: undefined symbol: libssh2_agent_disconnect In addition: Warning message: package "methods" in options("defaultPackages") was not found Error : package 'grDevices' does not have a namespace In addition: Warning messages: 1: package 'utils' in options("defaultPackages") was not found 2: package 'grDevices' in options("defaultPackages") was not found Error : package 'grDevices' does not have a namespace In addition: Warning message: package 'graphics' in options("defaultPackages") was not found Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/methods/libs/methods.so':
/usr/lib64/R/library/methods/libs/methods.so: undefined symbol: libssh2_agent_disconnect In addition: Warning message: package 'stats' in options("defaultPackages") was not found During startup - Warning message: package 'methods' in options("defaultPackages") was not found
What' about this error ? I couldn't any function. For example;
install.packages("test")
Error: could not find function "install.packages"
Thanks
updating libssh2 fixed this problem for me
below , i am sharing my experience installing R as i had a somehow similar problem , that was resolved after quite some fooling around by simply updating the libssh2 package !
installed R version 3 , once started it throws various errors about failure to load shared objects , each of those ends with the magic error "undefined symbol: libssh2_exit" , i tried to find out what is wrong with those objects , and i tried to force load them using ldconfig , but all my attempts went in vain ! the files exist and they dont look to be corrupted in anyway
{
[root@Centos6-vtl-sb ~]# R
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/methods/libs/methods.so':
/usr/lib64/R/library/methods/libs/methods.so: undefined symbol: libssh2_exit
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/utils/libs/utils.so':
/usr/lib64/R/library/utils/libs/utils.so: undefined symbol: libssh2_exit
In addition: Warning message:
package "methods" in options("defaultPackages") was not found
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
/usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: libssh2_exit
In addition: Warning message:
package "utils" in options("defaultPackages") was not found
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
/usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: libssh2_exit
In addition: Warning message:
package "grDevices" in options("defaultPackages") was not found
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/grDevices/libs/grDevices.so':
/usr/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: libssh2_exit
In addition: Warning message:
package "graphics" in options("defaultPackages") was not found
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/R/library/methods/libs/methods.so':
/usr/lib64/R/library/methods/libs/methods.so: undefined symbol: libssh2_exit
In addition: Warning message:
package "stats" in options("defaultPackages") was not found
During startup - Warning message:
package "methods" in options("defaultPackages") was not found
> quit()
Save workspace image? [y/n/c]: n
[root@Centos6-vtl-sb ~]# ls /usr/lib64/R/library/methods/libs/methods.so
/usr/lib64/R/library/methods/libs/methods.so
[root@Centos6-vtl-sb ~]#
}
Finally i decided to check the libssh2 version , to find that my version is a modern version , and once i updated it , those errors just vanished
{
[root@Centos6-vtl-sb ~]# yum whatprovides libssh2
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
* base: mirror.steadfast.net
* centosplus: mirror.steadfast.net
* elrepo: mirrors.ircam.fr
* epel: ftp.upjs.sk
* extras: mirror.steadfast.net
* updates: mirror.steadfast.net
libssh2-1.4.2-2.el6_7.1.x86_64 : A library implementing the SSH2 protocol
Repo : base
Matched from:
libssh2-1.4.2-2.el6_7.1.i686 : A library implementing the SSH2 protocol
Repo : base
Matched from:
libssh2-1.2.2-7.el6.x86_64 : A library implementing the SSH2 protocol
Repo : installed
Matched from:
Other : Provides-match: libssh2
[root@Centos6-vtl-sb ~]# rpm -qa | grep -i libssh
libssh2-1.2.2-7.el6.x86_64
[root@Centos6-vtl-sb ~]#
[root@Centos6-vtl-sb ~]#
[root@Centos6-vtl-sb ~]# yum update libssh2
.......
[root@Centos6-vtl-sb ~]# R
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> quit()
Save workspace image? [y/n/c]: y
[root@Centos6-vtl-sb ~]#
}
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