On 5/19/20 1:54 PM, Kevin Ushey wrote:
The main thing that stands out to me in that error:
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
R bundles its own copies of libquadmath and libgcc:
kevinushey@Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib
$ ls -la
total 19120
drwxrwxr-x 11 root admin 352 Apr 24 03:23 .
drwxrwxr-x 18 root admin 576 Apr 29 11:46 ..
-rwxrwxr-x 1 root admin 4070896 Apr 24 03:23 libR.dylib
drwxrwxr-x 3 root admin 96 Apr 24 03:22 libR.dylib.dSYM
-rwxrwxr-x 1 root admin 201472 Apr 24 03:23 libRblas.dylib
drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRblas.dylib.dSYM
-rwxrwxr-x 1 root admin 2181472 Apr 24 03:23 libRlapack.dylib
drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRlapack.dylib.dSYM
-rw-rw-r-- 1 root admin 160624 Apr 24 03:23 libgcc_s.1.dylib
-rwxrwxr-x 1 root admin 2851008 Apr 24 03:23 libgfortran.5.dylib
-rwxrwxr-x 1 root admin 309648 Apr 24 03:23 libquadmath.0.dylib
which should normally be used during the link step. However, versions in
/usr/local/lib are being discovered instead, which presumably aren't
compatible.
Kevin;
Is that the sort of situation that might be cause by mixing
homebrew-compiled and R.Framework-compiled packages?
David.
The simplest fix is (likely) to move those files out of the way. Otherwise,
you'd likely have to muck around with Makevars / Makeconf to adjust the
linker flags so the correct versions of these libraries are found.
Best,
Kevin
On Tue, May 19, 2020 at 6:46 AM Adelchi Azzalini <azzal...@stat.unipd.it>
wrote:
Hi.
In essence, my problem is that I cannot install a package which requires
Fortran-77 compilation on my Mac.
More in detail, this is my own package 'mnormt' which exists on CRAN since
2006; it is currently at version 1.5-7. It has been developed in successive
versions on a Linux machine, where it compiles with no problems. The macOS
and MS-windows versions are created on CRAN, where it passes all pertaining
checks.
Now, in the new pandemic world, I need create a new version of the
package, but working from home, hence using my Mac laptop instead of the
Linux desktop as in the past. Unfortunately, compilation or loading does
not work. If I run
R CMD check mnormt_1.5-7.tar.gz
first I get a bunch of warning messages such as
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4)
.... [-Wconversion]
Warning: ‘lxchng’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
Warning: Label 10 at (1) defined but not used [-Wunused-label]
and finally it crashes with
Error: package or namespace load failed for ‘mnormt’:
.onLoad failed in loadNamespace() for 'mnormt', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':
dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
6): Symbol not found: ___addtf3
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
in /usr/local/lib/libquadmath.0.dylib
Error: loading failed
Needless to say, I have no idea what this "addtf3" is or it should be.
There is no such a symbol in the Fortran code.
I believe to have installed all ingredients indicated at
https://mac.r-project.org/tools/
See the list below with details about my system and other installed tools.
Any suggestions for sorting this out?
Adelchi Azzalini
---------------------------------------------------
Installation info:
R> R.version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.0
year 2020
month 04
day 24
svn rev 78286
language R
version.string R version 4.0.0 (2020-04-24)
nickname Arbor Day
--- macOS Mojave 10.14.6
--- Xcode version 11.3.1
--- Fortran
[aa@mac-2013:~] gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper
Target: x86_64-apple-darwin18
Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran
--with-gmp=/Users/fx/devel/gcc/build_package/deps
--enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18
--disable-multilib --with-native-system-header-dir=/usr/include
--with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
gcc version 8.2.0 (GCC)
[aa@mac-2013:~] echo $PATH
.:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin
-- other tools indicated at https://mac.r-project.org/tools/
xz-5.2.5/ is installed
PCRE2 10.34 built with --disable-jit
bzip2 Version 1.0.6 is installed
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