[Bug 223200] math/R with OPENBLAS, openblas is not linked or used.

[bugzilla-noreply at freebsd.org]

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=223200

            Bug ID: 223200
           Summary: math/R with OPENBLAS, openblas is not linked or used.
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: Individual Port(s)
          Assignee: jrm at freebsd.org
          Reporter: ebs15242 at gmail.com
          Assignee: jrm at freebsd.org
             Flags: maintainer-feedback?(jrm at freebsd.org)

Enabled OPENBLAS, config told me FLANG was not supported, so I enabled
GFORTRAN.

$ pkg info R | grep 'BLAS\|FORTRAN'
        GFORTRAN       : on
        OPENBLAS       : on
        RBLAS          : off

Built successfully.  Blas is not mentioned in sessionInfo()

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: amd64-portbld-freebsd11.0 (64-bit)
Running under: FreeBSD bio 11.0-STABLE FreeBSD 11.0-STABLE #0
r321665+25fe8ba8d06(freenas/11.0-stable): Mon Sep 25 06:24:11 UTC 2017    
root at gauntlet:/freenas-11-releng/freenas/_BE/objs/freenas-11-releng/freenas/_BE/os/sys/FreeNAS.amd64
 amd64

Matrix products: default
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
[1] C

Nor is it being used by a running R process. 

$ lsof | grep -i blas
lsof: WARNING: compiled for FreeBSD release 11.0-RELEASE-p13; this is
11.0-STABLE.
$

It appears to not have even been linked. 

$ ldd /usr/local/lib/R/library/stats/libs/stats.so
/usr/local/lib/R/library/stats/libs/stats.so:
        libRlapack.so => not found (0)
        libgfortran.so.3 => /usr/local/lib/gcc6/libgfortran.so.3 (0x8012ba000)
        libm.so.5 => /lib/libm.so.5 (0x8015e2000)
        libquadmath.so.0 => /usr/local/lib/gcc6/libquadmath.so.0 (0x80180d000)
        libR.so.3.4 => not found (0)
        libc.so.7 => /lib/libc.so.7 (0x800823000)
        libgcc_s.so.1 => /usr/local/lib/gcc6/libgcc_s.so.1 (0x801a4c000)
$ ldd /usr/local/lib/R/lib/libR.so
/usr/local/lib/R/lib/libR.so:
        libgfortran.so.3 => /usr/local/lib/gcc6/libgfortran.so.3 (0x801613000)
        libm.so.5 => /lib/libm.so.5 (0x80193b000)
        libquadmath.so.0 => /usr/local/lib/gcc6/libquadmath.so.0 (0x801b66000)
        libintl.so.8 => /usr/local/lib/libintl.so.8 (0x801da5000)
        libreadline.so.7 => /usr/local/lib/libreadline.so.7 (0x801faf000)
        libpcre.so.1 => /usr/local/lib/libpcre.so.1 (0x8021ff000)
        liblzma.so.5 => /usr/lib/liblzma.so.5 (0x802477000)
        libbz2.so.4 => /usr/lib/libbz2.so.4 (0x8026a0000)
        libz.so.6 => /lib/libz.so.6 (0x8028b5000)
        librt.so.1 => /usr/lib/librt.so.1 (0x802acc000)
        libicuuc.so.59 => /usr/local/lib/libicuuc.so.59 (0x802cd1000)
        libicui18n.so.59 => /usr/local/lib/libicui18n.so.59 (0x803200000)
        libc.so.7 => /lib/libc.so.7 (0x800823000)
        libgcc_s.so.1 => /usr/local/lib/gcc6/libgcc_s.so.1 (0x8036b2000)
        libncursesw.so.8 => /lib/libncursesw.so.8 (0x8038c8000)
        libthr.so.3 => /lib/libthr.so.3 (0x803b24000)
        libicudata.so.59 => /usr/local/lib/libicudata.so.59 (0x803d4b000)
        libc++.so.1 => /usr/lib/libc++.so.1 (0x803f4c000)
        libcxxrt.so.1 => /lib/libcxxrt.so.1 (0x80420b000)


Openblas did make and install.

$ pkg info openblas
openblas-0.2.20_1,1
Name           : openblas
Version        : 0.2.20_1,1
Installed on   : Mon Oct 23 12:14:23 2017 PDT


After installation, on running R, stats.so complained about not finding
libRlapack.so.  I had to manually copy it to /usr/local/lib/R/lib/. I don't
know if this is related, but I thought I'd mention it.  It does not complain at
all about missing BLAS.

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