[Rcpp-devel] RcppArmadillo inv() depends on Lapack, zgetri_ not available on CRAN / R-forge?
baptiste.auguie at googlemail.com
Sun Jun 5 23:56:30 CEST 2011
Thank you for the explanations below.
On 5 June 2011 10:40, Dirk Eddelbuettel <edd at debian.org> wrote:
> 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://email@example.com/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.
Unsurprisingly, it fails, with the same complaint as R-forge.
> | 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).
I see; so basically the user will always need to have a full LAPACK
installed. Here's one question then, if R-core didn't consider
necessary to include those particular functions from LAPACK,
presumably that means that R defines its own routines to solve linear
systems and invert matrices. Is there any possibility to use those
routines with Armadillo?
> | 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.
I just checked how RcppGSL does it, and well, this configure magic is
way above my head.
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