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
|
| ______________________________________________
| [email protected] 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.
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
