thr3ads.net - R devel - [Rd] R build BLAS/LAPACK debugging ('dgemmtr

If this information is useful, please help other people find it:
Share via:

Ben Bolker

2026-Jan-26 18:29 UTC

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

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 at 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.

Dirk Eddelbuettel

2026-Jan-26 18:52 UTC

head link

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

On 26 January 2026 at 13:29, Ben Bolker wrote:
|    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?)

Couple of things to try:

1) I would make sure you do have the corresponding -dev packages for
building, not just the runtime packages. I cannot look onto your machines.

2) I would simplify; my builds actually just say --with-blas --with-lapack as
the Debian (and Ubuntu and PopOS!) package management sets the right default,
usually. So if you want openblas, install the corresponding packages (and
these days there are several).

3) If you are really lost or mad, follow reproducible steps. My Debian
package setup is public, my Dockerfiles are public, I am sure the R
Installation and Admin manual has things to say.

Lastly, we probably should have this chat on r-sig-debian to not bore our
good friends using windows, macos, fedora, ...

Dirk

| 
|    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 at 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.

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

R devel - Jan 2026 - R build BLAS/LAPACK debugging ('dgemmtr_' undefined)

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

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