[Rd] R build BLAS/LAPACK debugging ('dgemmtr_' undefined)

[Ben Bolker]

   Hmm, good idea but that isn't seeming to help me?

../r-devel/configure --enable-R-shlib --enable-memory-profiling 
--with-blas=-lopenblas --with-lapack=-llapack | egrep "(lapack|blas)"

configure: WARNING: C23 support is unavailable
checking for dgemm_ in -lopenblas... yes
checking for dpstrf_ in -llapack... yes
config.status: creating src/extra/blas/Makefile
config.status: creating src/modules/lapack/Makefile

    Then `make` gives me the same error.  (I guess I could look at the 
rocker Dockerfiles and try to copy them exactly?)

   cheers
    Ben



On 2026-01-26 1:22 p.m., Dirk Eddelbuettel wrote:
> 
> On 26 January 2026 at 12:45, Ben Bolker wrote:
> |
> |    I'm sure I'm doing something dumb, but having trouble building R from
> | source on PopOS! 22.04 LTS (debian/Ubuntu 'jammy' derivative):
> | "undefined symbol: dgemmtr_" when trying to load stuff from LAPACK.
> |
> | R appears to find stuff at the configure step (FWIW I get the same error
> | below if I take out "with-blas=-lopenblas")
> |
> | $ ../r-devel/configure --enable-R-shlib --enable-memory-profiling
> | --with-blas=-lopenblas | grep blas
> | configure: WARNING: C23 support is unavailable
> | checking for dgemm_ in -lopenblas... yes
> | config.status: creating src/extra/blas/Makefile
> 
> FWIW in all my build script(s) (for local r-devel builds, or the Debian R
> package, or container builds from source) I explicitly set the --with-blas
> and the --with-lapack flags.  As dgemm() is (well known) LAPACK routine [1] I
> think you are "simply" forgetting to link with LAPACK here.
> 
> Cheers, Dirk
> 
> [1] https://www.netlib.org/lapack/explore-html/dd/d09/group__gemm_ga1e899f8453bcbfde78e91a86a2dab984.html
> 
> |
> | Then `make` fails with:
> |
> | byte-compiling package 'grDevices'
> | Warning in solve.default(rgb) :
> |    unable to load shared object '/home/bolker/R/r-build/modules//lapack.so':
> |    /home/bolker/R/r-build/lib/libRlapack.so: undefined symbol: dgemmtr_
> | Error in solve.default(rgb) : LAPACK routines cannot be loaded
> |
> |    I do see a NEWS item from R 4.5.0
> | https://github.com/r-devel/r-svn/blob/42e81d981a540f4afc01d1002a64ab347eb5dc15/doc/NEWS.Rd#L956-L961
> | (I thought things were working until recently, but I haven't re-built
> | from scratch in a while ...)
> |
> | \item This update was mainly bug fixes but contained a barely
> |        documented major change.  The set of BLAS routines had been
> |        unchanged since 1988, so throughout \R's history.  This update
> |        introduced new BLAS routines \code{dgemmtr} and \code{zgemmtr}
> |        which are now used by LAPACK routines.  This means that BLAS
> |        implementations are no longer interchangeable.
> |
> | Section A.3.1
> | https://rstudio.github.io/r-manuals/r-admin/Essential-and-useful-other-programs-under-a-Unix-alike.html:
> |
> |  > The configure code checks that the external BLAS is complete (as of
> | LAPACK 3.9.1: it must include all double precision and double complex
> | routines, as well as LSAME), and appears to be usable. However, an
> | external BLAS has to be usable from a shared object (so must contain
> | position-independent code), and that is not checked.
> |
> |    I'd be surprised if by BLAS libraries *didn't* contain PIC, but ... ??
> |
> |    Suggestions for diagnostics/debugging welcome ...
> |
> |    cheers
> |     Ben Bolker
> |
> | ______________________________________________
> | R-devel using r-project.org mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-devel
> 

-- 
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Associate Chair (Graduate), Department of Mathematics & Statistics
Director, School of Computational Science and Engineering
> E-mail is sent at my convenience; I don't expect replies outside of working hours.