Dear All, I am building R from source[1], following what is done in "rules" for building Debian's R. But the R I generate, in contrast to the standard Debian's R, will not change the BLAS and LAPACK libraries it uses when I change them via "update-alternatives". I have no idea what I am doing wrong (but, somehow, I've been quite capable of making the same mistake(s) in three different machines).
I can "solve" the issue by running configure with --with-blas="-lblas" --with-lapack="-llapack" but I do not understand why I need to do this, when Dirk's configure in rules is using just --with-blas --with-lapack (and this is also what I understand I should be doing from section A.3.1 of "R Installation and Administration" ---https://cran.r-project.org/doc/manuals/r-release/R-admin.html#BLAS). This concerns me in so far as it suggests that I am missing something rather obvious. Thanks, R. Details of the steps I am following. 1. update-alternatives: use Atlas (lower priority than OpenBLAS) update-alternatives --config libblas.so.3-x86_64-linux-gnu There are 3 choices for the alternative libblas.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/li Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 95 auto mode * 1 /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 manual mode 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 95 manual mode update-alternatives --config liblapack.so.3-x86_64-linux-gnu There are 3 choices for the alternative liblapack.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/ 3). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3 95 auto mode * 1 /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 manual mode 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3 95 manual mode 2. Just in case, run /sbin/ldconfig 3. No LD_LIBRARY_PATH in env. 4. Configure: ./configure --with-blas --with-lapack --enable-R-shlib --without-recommended-packages 5. Interestingly, this picks up OpenBLAS: configure: searching for an external BLAS configure: searching for BLAS in default libraries checking for dgemm_... no configure: searching for OpenBLAS and R is now configured for x86_64-pc-linux-gnu (...) External libraries: pcre2, readline, BLAS(OpenBLAS), LAPACK(in blas), curl Options enabled: shared R library, R profiling (...) Options not enabled: shared BLAS, memory profiling 6. After make is finished, ldd: libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007f01b1ac2000) libatlas.so.3 => /usr/lib/x86_64-linux-gnu/libatlas.so.3 (0x00007f01b0f57000) And no openblas in any line. 7. sessionInfo shows it is using OpenBLAS Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-openmp/libopenblasp-r0.3.25.so; LAPACK version 3.11.0 8. R CMD config shows difference in the configuration - My build: ./R CMD config BLAS_LIBS: -lopenblas - ./R CMD config LAPACK_LIBS: nothing - Debian's R - /usr/bin/R CMD config BLAS_LIBS: -lblas - /usr/bin/R CMD config LAPACK_LIBS: -llapack [1] Why am I building from source? To match the exact version in BioConductor devel and for a cluster where I am playing with some compiler options -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-31 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com r.d...@uam.es ramon.d...@iib.uam.es https://ligarto.org/rdiaz _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
