SCIENTIFIC-LINUX-USERS Archives

July 2018

SCIENTIFIC-LINUX-USERS@LISTSERV.FNAL.GOV

Options: Use Monospaced Font
Show Text Part by Default
Show All Mail Headers

Message: [<< First] [< Prev] [Next >] [Last >>]
Topic: [<< First] [< Prev] [Next >] [Last >>]
Author: [<< First] [< Prev] [Next >] [Last >>]

Print Reply
Subject:
From:
"Lofgren, Eric" <[log in to unmask]>
Reply To:
Lofgren, Eric
Date:
Wed, 25 Jul 2018 21:57:04 +0000
Content-Type:
multipart/signed
Parts/Attachments:
text/plain (2474 bytes) , smime.p7s (1489 bytes)
Bruce,

It’s good advice, and yeah, a number of accounts are being downgraded.

The good news is that this was an easy fix - RStudio Server needed an update to it’s LD_LIBRARY_PATH.

Eric

> On Jul 25, 2018, at 2:40 PM, Bruce Ferrell <[log in to unmask]> wrote:
> 
> On 07/25/2018 12:57 PM, Lofgren, Eric wrote:
>> The trials and travails of my poor server continue. The hard drive upgrade went well, but right after it was done, some students on the server got…creative. One of them updated what version of gcc was on it for another project.
>> 
>> One of the primary purposes of the machine is to work as an RStudio server, and when I attempted to install Rcpp, I got the following error:
>> 
>> Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so': /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so)
>> Error: loading failed Execution halted ERROR: loading failed
>> 
>> Oddly, this doesn't occur when using R from the command line, which makes me think that RStudio Server is having trouble finding GLIBCXX_3.4.20, rather than it being genuinely missing.
>> 
>> Does anyone know how to sort this error out?
>> 
>> Thanks,
>> Eric
> 
> First thing  run
> 
> ldd /home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so
> 
> This will show you the other linked libraries that library file needs
> 
> You'll see something like "not found" next to missing libraries. This will include version mismatches.
> 
> Next run
> 
> rpm -qf /lib64/libstdc++.so.6
> 
> That will show you version it is.  Your "creative" student may have known enough to be dangerous (used yum to resolve dependencies) and when s/he did the gcc version change, it may have made changes other required packages.
> 
> final thing.  take root access away.  This includes sudo unless it's heavily restricted.
> 
> If your server has sufficient resource, you might consider giving students VMs to fiddle in to prevent them burning down Rome.
> 
> I use Virtualbox because it's fast and easy.  KVM works too.
> 
> I avoid xen as it has bitten me too many times.
> 
> I refuse to use VMware/ESXi.  It's pricey and while common in the corporate world, I've found it to be just a wee touch brain dead.
> 
> 



ATOM RSS1 RSS2