[R] Common install of R on network disk

[John McKown]

On Tue, Jul 7, 2015 at 2:42 AM, Lionel SPINELLI <spinelli at ciml.univ-mrs.fr>
wrote:

> Hello all,
>
>
> I am looking for information on how to install R on a network disk so that
> it can be used by several users mounting this network disk from different
> computers.
>
> We are using a cluster and shared computers in my lab. Those machines can
> mount network disks. On those disks we have installed several tools, like
> samtools that can be used from any user and from any machine since they
> have installs that do no required any system libraries.
>
> We would like to do the same thing with R: have a folder in the network
> disk that contains R (and its libraries) and that permits to execute it
> from any machine that mount the network disk. However, it seems R uses
> system libraries since, once the installation done we obtain the following
> message when trying to execute it from a different machine than the one
> from which R was installed:
>
>  error while loading shared libraries: libicuuc.so.52: cannot open shared
> object file: No such file or directory
>
> This library seems present on the machine executing R but seems not found
> the same. We did not found any info on how to set a lib path in order to
> put that library with the R install.
>
> Do you know any reference that explain how to successfully achieved the R
> install as we would like to?
>
>
> Thanks a lot in advance
>
>
First, I am assuming that all the clients are running the same OS at the
same, or compatible, levels. I am also assuming Linux, but that may be
pushing it. What I _think_ will work (I can't test it where I am now) is to
set the LD_LIBRARY_PATH environment to include the directory which contains
the libicuuc.so file.

For a possible example, suppose libicucc.so is in the directory
/network/disk/R-installation/lib, then try the command (I am using BASH):

LD_LIBRARY_PATH="${LD_LIBRARY_PATH}${LD_LIBRARY_PATH+:}/network/disk/R-installation/lib"
R

Yes, the above is _ugly_. An easier way might be do to the following (as
root) on all the systems which want to run R (# is the command prompt for
"root", not something you type in!)

# echo "/netwrok/disk/R-installation/lib" >>/etc/ld.so.conf.d/R-network.conf
# ldconfig

What the above does is add the directory /network/disk/R-installation/lib
(which contains the R shared libraries) to the directories automatically
searched for shared libraries. You can add more that one directory name,
each on a separate line, into the R-network.conf file. Oh, the name of the
file can be anything you like but must be in the directory
/etc/ld.so.conf.d and end in ".conf". E.g. R-network.conf or
myIdiotBrother.conf would both work.

# echo "/network/disk1/R-installation/lib"
>>/etc/ld.so.conf.d/R-network.conf
# echo "/network/disk2/R-2nd/lib" >>/etc/ld.so.conf.d/R-network.conf
# echo "/some/other/directory/entirely" >>/etc/ld.so.conf.d/R-network.conf
# ldconfig

would add the three mentioned directories.


This stackoverflow discussion might be of some help as well:
http://stackoverflow.com/questions/13428910/how-to-set-the-environmental-variable-ld-library-path-in-linux





>
> [http://sesame.univ-amu.fr/Logos/logo_sciences.jpg]
>
> Lionel Spinelli - Ingénieur de recherche en bioinformatique
> UMR_S 1090 TAGC  et  UMR_S 1104 CIML
>
> Aix-Marseille Université - LUMINY - 163 Avenue de Luminy - 13009 Marseille
>
> Tél: +33(0)4 91 82 87 12 (TAGC) / +33(0)4 91 26 91 90 (CIML)
>
> Site : http://www.univ-amu.fr<http://www.univ-amu.fr/> - Email :
> lionel.spinelli at univ-amu.fr<mailto:lionel.spinelli at univ-amu.fr>
>
>
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Maranatha! <><
John McKown

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