[R] Compilation problems with R4.4.0

[Simon Andrews]

The lapack parts of the configure are:

checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -llapack... no
checking for ATLAS routines in liblapack... no
checking for dpstrf_ in -llapack... yes
checking for liblapack dependency with both BLAS and LAPACK routines... no
checking if LAPACK version >= 3.9.0... 3.9.0, so yes
checking for iconv.h... yes
checking for iconv... yes

The lapack libraries are:

$ rpm -qa | grep lapack
lapack-3.9.0-10.el9.x86_64
lapack64_-3.9.0-10.el9.x86_64
lapack64-3.9.0-10.el9.x86_64
lapack-devel-3.9.0-10.el9.x86_64

-----Original Message-----
From: Ivan Krylov <ikrylov using disroot.org> 
Sent: 08 May 2024 16:09
To: Simon Andrews <simon.andrews using babraham.ac.uk>
Cc: Simon Andrews via R-help <r-help using r-project.org>; Miguel Esteva <esteva.m using wehi.edu.au>
Subject: Re: [R] Compilation problems with R4.4.0

В Wed, 8 May 2024 14:25:08 +0000
Simon Andrews <simon.andrews using babraham.ac.uk> пишет:

> #8  0x00007ffff3f87c0b in dgesv (
>  n=12884901891, nrhs=4294967299,
>  a=<error reading variable: value has been optimized out>,  
> lda=12884901891, ipiv=...,  b=<error reading variable: value has been 
> optimized out>,  ldb=12884901891, info=0
> ) at /usr/src/debug/lapack-3.9.0-10.el9.x86_64/SRC/dgesv.f:167
> #9 0x00007ffff50b2a17 in La_solve (
>  tolin=<optimized out>, Bin=<optimized out>, A=0x18f2f68
> ) at Lapack.c:1246
> #10 mod_do_lapack (
>  call=<optimized out>, op=<optimized out>, args=<optimized out>,  
> env=<optimized out>
> ) at Lapack.c:1483

It looks like this R build is linked to a LAPACK. I now also notice
LAPACK(generic) in the list of external libraries in your ./configure output. I've tried to link R to AlmaLinux's builds of reference BLAS and LAPACK using --with-blas='-l:libblas.so.3'
--with-lapack='-l:liblapack.so.3' (where do I get libblas.so on AlmaLinux?), but that doesn't crash either.

What does the config.log currently say about your BLAS and LAPACK situation? It's a number of lines between

configure:47012: checking whether 'struct tm' includes tm_gmtoff

and

configure:48858: checking for iconv.h.

If you'd like to link your R to custom BLAS and LAPACK, try specifying the necessary linker flags explicitly with --with-blas=-lwhatever, --with-lapack=-lwhatever. If you're fine with reference BLAS & LAPACK that come with R, try ./configure --without-blas --without-lapack.
Normally, R's ./configure tries to prevent linking to an external LAPACK without linking to an external BLAS; I'm not sure how it got you
LAPACK(generic) without BLAS(generic).

--
Best regards,
Ivan

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