[R-sig-Debian] custom built R will not change BLAS/LAPACK with update-alternatives

[Dirk Eddelbuettel]

If you match the exact build-deps I use and the exact options from
debian/rules you should end up with the exact same output. As that is whay
you desire but do not get we need to drill down into where it deviates. FWIW
last time I build the Debian the (relevant) part (of the large) configure log
was below.  What do you get for BLAS/LAPACK?


R is now configured for x86_64-pc-linux-gnu

  Source directory:            .
  Installation directory:      /usr

  C compiler:                  gcc  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  Fortran fixed-form compiler: gfortran  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -fcf-protection

  Default C++ compiler:        g++ -std=gnu++17  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  C++11 compiler:              g++ -std=gnu++11  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  C++14 compiler:              g++ -std=gnu++14  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  C++17 compiler:              g++ -std=gnu++17  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  C++20 compiler:              g++ -std=gnu++20  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  C++23 compiler:              g++ -std=gnu++23  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
  Fortran free-form compiler:  gfortran  -g -O2 -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -fcf-protection
  Obj-C compiler:	        

  Interfaces supported:        X11, tcltk
  External libraries:          pcre2, readline, BLAS(generic), LAPACK(generic), curl
  Additional capabilities:     PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:             shared R library, R profiling, memory profiling

  Capabilities skipped:        
  Options not enabled:         shared BLAS

  Recommended packages:        no


Despite the display of 'shared BLAS' not enabled, I still have

root using fb498fe53700:/# ldd /usr/lib/R/modules/lapack.so 
        linux-vdso.so.1 (0x00007ffcb09c7000)
        libR.so => /lib/libR.so (0x00007ff7dd7f1000)
        liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3 (0x00007ff7dd0f6000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff7dd017000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff7dce36000)
        libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x00007ff7dcdd3000)
        libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8 (0x00007ff7dcd7b000)
        libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007ff7dccdf000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007ff7dccb0000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007ff7dcc9d000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007ff7dcc7e000)
        libtirpc.so.3 => /lib/x86_64-linux-gnu/libtirpc.so.3 (0x00007ff7dcc50000)
        libicuuc.so.72 => /lib/x86_64-linux-gnu/libicuuc.so.72 (0x00007ff7dca52000)
        libicui18n.so.72 => /lib/x86_64-linux-gnu/libicui18n.so.72 (0x00007ff7dc726000)
        libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007ff7dc6de000)
        /lib64/ld-linux-x86-64.so.2 (0x00007ff7ddc74000)
        libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007ff7da3f0000)
        libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007ff7da126000)
        libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00007ff7da0f3000)
        libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007ff7da0a1000)
        libicudata.so.72 => /lib/x86_64-linux-gnu/libicudata.so.72 (0x00007ff7d82cf000)
        libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007ff7d80b5000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ff7d8095000)
        libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007ff7d804e000)
        libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007ff7d7f74000)
        libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007ff7d7f47000)
        libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007ff7d7f41000)
        libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007ff7d7f33000)
        libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007ff7d7f2c000)
        libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007ff7d7f1b000)
root using fb498fe53700:/# ls -l /lib/x86_64-linux-gnu/liblapack.so.3
lrwxrwxrwx 1 root root 49 Nov 27  2022 /lib/x86_64-linux-gnu/liblapack.so.3 -> /etc/alternatives/liblapack.so.3-x86_64-linux-gnu
root using fb498fe53700:/# ls -l /lib/x86_64-linux-gnu/libblas.so.3
lrwxrwxrwx 1 root root 47 Nov 27  2022 /lib/x86_64-linux-gnu/libblas.so.3 -> /etc/alternatives/libblas.so.3-x86_64-linux-gnu
root using fb498fe53700:/# 

the /etc/alternatives mechanism you are after. (That was from rocker/r-base,
a quick way for me to get to clean and current Debian build.)

Dirk

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