mgcv won't load - R-SIG-Debian

Fri, Apr 22, 2011 12:40 PM #

Hi,

I'm getting the following error when I try and load mgcv:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/lib/R/library/Matrix/libs/Matrix.so':
  /usr/lib/R/library/Matrix/libs/Matrix.so: undefined symbol: R_check_class_and_super
Error: package/namespace load failed for 'mgcv'

I thought there might be a mismatch between packages from cran2deb,
install.packages() and the main R repos, so I purged my R installation
and rm-ed all the locally-installed packages and reinstalled, using only
the official R repos. Same errors. 

Anyone else seeing this? Any ideas how to fix it?

Thanks,

Tyler
Debian Testing
R version 2.12.2 (2011-02-25)
Linux 2.6.32-5-686

Cedrick Johnson

Fri, Apr 22, 2011 12:57 PM #

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Tyler Smith

Fri, Apr 22, 2011 1:11 PM #

"Johnson, Cedrick W." <cedrick at cedrickjohnson.com> writes:

Thanks, but I've already tried that. I just found a very brief blog
post[1] indicating that there were incompatibilities between packages
that depend on the most recent version of Matrix and versions of R <
2.13. I've updated to R.13 from the unstable repositories and now all
appears to work again.

As long as R 2.13 makes it into testing before some new conflict arises
on my now mixed system!

Cheers,

Tyler


http://thiagogm.wordpress.com/2011/04/13/problems-with-r-package-matrix/

Dirk Eddelbuettel

Fri, Apr 22, 2011 1:39 PM #

On 22 April 2011 at 16:11, Tyler Smith wrote:

| "Johnson, Cedrick W." <cedrick at cedrickjohnson.com> writes:
| 
| > see if you can install r-cran-matrix from the repository perhaps...
| >
| > -c
| 
| Thanks, but I've already tried that. I just found a very brief blog
| post[1] indicating that there were incompatibilities between packages
| that depend on the most recent version of Matrix and versions of R <
| 2.13. I've updated to R.13 from the unstable repositories and now all
| appears to work again.

Hm, sounds like you may have found a bug in Depends being too loose...

Just for the record, did you take r-cran-mgcv and r-cran-matrix from Debian
or did you mix and match with direct CRAN installations? 

| As long as R 2.13 makes it into testing before some new conflict arises
| on my now mixed system!

Should happen in two days once the usual 'ten day minimum' is reached (and no
important bugs are open, or build issue arose) as per 

	http://qa.debian.org/excuses.php?package=r-base

So all should be well.

Dirk

Gauss checked the infinity of primes by counting them, starting 
from the last.                     -- http://www.gaussfacts.com

Tyler Smith

Fri, Apr 22, 2011 1:57 PM #

Dirk Eddelbuettel <edd at debian.org> writes:

My current working system includes mostly debian packages in
/usr/lib/R/library/ (including mgcv and Matrix), some additional debian
packages in /usr/lib/R/site-library, and 10 packages in
/usr/local/lib/R/site-library that are not in the Debian repositories.

To be honest, I'm after spending more time than I'd like this afternoon
googling, I'm a little confused as to what the current best practices
are. I decided to re-install everything, using r-cran- packages when
available, and using install.packages() from within R only when they
aren't.

Good news!

Thanks,

Tyler