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

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: undefined symbol:

| > |
| > | It builds fine on my local machines (Mac OS 10.5, 10.6).
| > |
| > | >From an older discussion on this list <
| > |

| > | the issue seems to be that Armadillo's inv() relies on a function

| > | is not provided by R, only by LAPACK. I have just replaced inv()

| > | pinv() and solve() in my code; merely to see what happens, but

| > | 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

what feature of the full Armadillo are lacking in RcppArmadillo.

| > Sometime relatively early in the RcppArmadillo development process,

| > convinced Romain and myself to go for a pure template solution with

| > as all / most things found during the configure (or in this case,

| > stage can be assumed 'found' given that we have around us by design.

| > 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

| > and shipping a library, having to tell users how to set PKG_LIBS etc

| > firmly believe that this helped tremendously in getting

| > 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.

| > likely to be a dicey situation as you per se do not know whether R

| > and linked with its own (subset) copy of LAPACK, or whether it uses

| > LAPACK libraries (as e.g. the Debian / Ubuntu systems do).  So you

| > a spot bother and I not sure what I can recommend --- other than

| > luck at some short configure snippets that will run at package build

| > determine whether the system you want to build cda on it 'rich'

| > support it.  I can help you off list with some configure snippets as

| > my packages have configure code; adding a test for zgetri should be

| >
| > | Does anybody have any experience
| > | dealing with such issues w.r.t releasing a package on R-forge /

| > | 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

| > matter of making your package installable on the largest number of

| > systems.  Also try win-builder.r-project.org to see how it fares on

| > 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,

generally not the case. Many OSs (Linux incl) ship source only and

link dynamically, others (Windoze) use dynamic linking and OS X is for

know somewhere in the middle (as you can get prebuild packages with

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

the GSL.

I just checked how RcppGSL does it, and well, this configure magic is
way above my head.

Best,

baptiste