[Rcpp-devel] RcppArmadillo inv() depends on Lapack, zgetri_ not available on CRAN / R-forge?

Dirk Eddelbuettel edd at debian.org
Sun Jun 5 00:40:02 CEST 2011

On 5 June 2011 at 10:12, baptiste auguie wrote:
| Hi Dirk and all,
| On 4 June 2011 12:04, Dirk Eddelbuettel <edd at debian.org> wrote:
| >
| > Baptiste,
| >
| > On 4 June 2011 at 11:45, baptiste auguie wrote:
| > | Dear list,
| > |
| > | My package cda, which I was hoping to release on CRAN, fails to
| > | compile on R-forge with error,
| > |
| > | ** testing if installed package can be loaded
| > | Error in dyn.load(file, DLLpath = DLLpath, ...) :
| > |   unable to load shared object '/tmp/RtmpbztUMm/Rinst1829c04c/cda/libs/cda.so':
| > |   /tmp/RtmpbztUMm/Rinst1829c04c/cda/libs/cda.so: undefined symbol: zgetri_
| > |
| > | It builds fine on my local machines (Mac OS 10.5, 10.6).
| > |
| > | >From an older discussion on this list <
| > | http://www.mail-archive.com/rcpp-devel@lists.r-forge.r-project.org/msg00678.html>
| > | the issue seems to be that Armadillo's inv() relies on a function that
| > | is not provided by R, only by LAPACK. I have just replaced inv() by
| > | pinv() and solve() in my code; merely to see what happens, but chances
| > | are they also require a full LAPACK.
| Indeed, the error on R-forge is now with zgels_, required to solve
| linear systems. It seems one cannot solve Armadillo linear systems
| without LAPACK in the current situation.

Yes. Doug, Romain and myself should address that, or at least make it clear
what feature of the full Armadillo are lacking in RcppArmadillo.
| > Sometime relatively early in the RcppArmadillo development process, Doug
| > convinced Romain and myself to go for a pure template solution with Armadillo
| > as all / most things found during the configure (or in this case, cmake)
| > stage can be assumed 'found' given that we have around us by design.  So no
| > testing, no local library and full reliance and what R gives us.
| >
| > That was a brilliant idea, and has freed us from having to rely on building
| > and shipping a library, having to tell users how to set PKG_LIBS etc pp and I
| > firmly believe that this helped tremendously in getting RcppArmadillo more
| > widely used. So I would not want to revert this.
| It sounds like a good choice, I agree. Yet solving a linear system is
| quite a crucial task in linear algebra; it would be nice if we could
| come up with a tutorial recipe for dummies like me.
| >
| > In any event, it seems that you need more LAPACK than R has for you.  That is
| > likely to be a dicey situation as you per se do not know whether R was built
| > and linked with its own (subset) copy of LAPACK, or whether it uses system
| > LAPACK libraries (as e.g. the Debian / Ubuntu systems do).  So you may be in
| > a spot bother and I not sure what I can recommend --- other than trying your
| > luck at some short configure snippets that will run at package build time to
| > determine whether the system you want to build cda on it 'rich' enough to
| > support it.  I can help you off list with some configure snippets as some of
| > my packages have configure code; adding a test for zgetri should be feasible.
| >
| > | Does anybody have any experience
| > | dealing with such issues w.r.t releasing a package on R-forge / CRAN?
| > | Is there any chance they would consider installing LAPACK on those
| > | servers, or is there no point in asking such things?
| >
| > I don't think it is a matter of fixing the R-Forge server. I think it is a
| > matter of making your package installable on the largest number of user
| > systems.  Also try win-builder.r-project.org to see how it fares on that
| > platform.
| I was under the impression that R-forge or CRAN, if it had LAPACK
| installed, could produce binaries for the relevant platforms, and
| users would not have to build the package themselves and would not be
| required of having LAPACK on their machine. That's probably a
| misconception, isn't it?

If and only statically linked binaries or libraries where produced, which is
generally not the case. Many OSs (Linux incl) ship source only and otherwise
link dynamically, others (Windoze) use dynamic linking and OS X is for all I
know somewhere in the middle (as you can get prebuild packages with dynamic
linking or build from source).
| Sorry for being dense, I don't know anything about linking R to
| external dependencies.

It can be done; there are many examples -- for example every package using
the GSL.


Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com

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