Failures in installing pymol-py36 on Catalina

Dear All,
I've just moved to MacOS Catalina on a new Mac laptop. I'm encountering several problems trying to install pymol-py36. I'm poorly skilled in Linux and Unix, so I'm just asking for explanations and, hopefully, for solutions.
A first failure on installing term-readkey-pm5184-2.37-1 was solved following the suggestion found here:

https://github.com/fink/fink-distributions/issues/461#issuecomment-563331868

that is changing

 "$archflags $perlcmd Makefile.PL \%c\n".
 "/usr/bin/make CC=gcc CXX=g++\n";

to


                                "$archflags $perlcmd Makefile.PL \%c\n".
                                "perl -pi -e 's, blib/, %b/blib/,g' Makefile\n".
                                "/usr/bin/make CC=gcc CXX=g++\n";

in opt/sw/lib/perl5/Fink/PkgVersion.pm

other packages could be installed then, but I' stuck on openblas. Here is the error message


marcopatrone@MBP-di-Marco ~ % sudo fink install pymol-py36

Scanning package description files..........

Information about 10248 packages read in 1 seconds.

Modifying fink-bld user and group.

The following package will be installed or updated:

 pymol-py36

The following 17 additional packages will be installed:

 cython-py36 dos2unix freeglut2 freeglut2-shlibs glew1.13 glew1.13-shlibs

 glew2.0 glew2.0-shlibs numpy-py36 openblas openblas-shlibs pmw2-py36 po4a

 python36 python36-shlibs scipy-py36 setuptools-tng-py36

Default answer will be chosen in 60 seconds...

Do you want to continue? [Y/n] y

Setting runtime build-lock...

dpkg-deb -b /opt/sw/src/fink.build/root-fink-buildlock-openblas-0.3.8-1 /opt/sw/src/fink.build

dpkg-deb: costruisco il pacchetto `fink-buildlock-openblas-0.3.8-1' in `/opt/sw/src/fink.build/fink-buildlock-openblas-0.3.8-1_2020.05.27-09.02.11_darwin-x86_64.deb'.

Installing build-lock package...

/opt/sw/bin/dpkg-lockwait -i /opt/sw/src/fink.build/fink-buildlock-openblas-0.3.8-1_2020.05.27-09.02.11_darwin-x86_64.deb

Selecting previously deselected package fink-buildlock-openblas-0.3.8-1.

(Reading database ... 32551 files and directories currently installed.)

Unpacking fink-buildlock-openblas-0.3.8-1 (from .../fink-buildlock-openblas-0.3.8-1_2020.05.27-09.02.11_darwin-x86_64.deb) ...

Setting up fink-buildlock-openblas-0.3.8-1 (2020.05.27-09.02.11) ...


sudo -u fink-bld [ENV] sh -c /tmp/fink.zGIwl

env LANG=C LC_ALL=C /opt/sw/bin/tar  --no-same-owner --no-same-permissions -xf /opt/sw/src/OpenBLAS-0.3.8.tar.gz

sudo -u fink-bld [ENV] sh -c /tmp/fink.YQtTs

[ -r /opt/sw/fink/dists/stable/main/finkinfo/sci/openblas.patch ]

sudo -u fink-bld [ENV] sh -c /tmp/fink.XS8yr

sed 's|@PREFIX@|/opt/sw|g' < /opt/sw/fink/dists/stable/main/finkinfo/sci/openblas.patch | patch -p1

Warning: Failed to set locale category LC_NUMERIC to en_IT.

Warning: Failed to set locale category LC_TIME to en_IT.

Warning: Failed to set locale category LC_COLLATE to en_IT.

Warning: Failed to set locale category LC_MONETARY to en_IT.

Warning: Failed to set locale category LC_MESSAGES to en_IT.

patching file Makefile.system

Hunk #3 succeeded at 1272 (offset -2 lines).

patching file benchmark/Makefile

patching file benchmark/smallscaling.c

patching file Makefile

patching file Makefile.install

patching file .travis.yml

patching file Makefile.prebuild

patching file Makefile.system

patching file c_check

sudo -u fink-bld [ENV] sh -c /tmp/fink.ay9V6

/tmp/fink.SPSMh

#!/bin/sh -ev

# set arch to minimum model supported in OS version

darwin_vers=$(uname -r | cut -d. -f1)

uname -r | cut -d. -f1

if [ "$darwin_vers" -ge 18 ]; then

perl -pi -e "s|(COMMON_OPT = -O2)|\$1 -mtune=cascadelake -march=ivybridge|g;" Makefile.system

else

perl -pi -e "s|(COMMON_OPT = -O2)|\$1 -mtune=cascadelake -march=core2|g;" Makefile.system

fi

make FC=gfortran-fsf-9 USE_THREAD=1 libs netlib shared

Warning: Failed to set locale category LC_NUMERIC to en_IT.

Warning: Failed to set locale category LC_TIME to en_IT.

Warning: Failed to set locale category LC_COLLATE to en_IT.

Warning: Failed to set locale category LC_MONETARY to en_IT.

Warning: Failed to set locale category LC_MESSAGES to en_IT.

Warning: Failed to set locale category LC_NUMERIC to en_IT.

Warning: Failed to set locale category LC_TIME to en_IT.

Warning: Failed to set locale category LC_COLLATE to en_IT.

Warning: Failed to set locale category LC_MONETARY to en_IT.

Warning: Failed to set locale category LC_MESSAGES to en_IT.

Warning: Failed to set locale category LC_NUMERIC to en_IT.

Warning: Failed to set locale category LC_TIME to en_IT.

Warning: Failed to set locale category LC_COLLATE to en_IT.

Warning: Failed to set locale category LC_MONETARY to en_IT.

Warning: Failed to set locale category LC_MESSAGES to en_IT.

Makefile:141: *** OpenBLAS: Detecting CPU failed. Please set TARGET explicitly, e.g. make TARGET=your_cpu_target. Please read README for the detail..  Stop.

### execution of /tmp/fink.SPSMh failed, exit code 2

### execution of /tmp/fink.ay9V6 failed, exit code 2

Removing runtime build-lock...

Removing build-lock package...

/opt/sw/bin/dpkg-lockwait -r fink-buildlock-openblas-0.3.8-1

(Reading database ... 32552 files and directories currently installed.)

Removing fink-buildlock-openblas-0.3.8-1 ...

Failed: phase compiling: openblas-0.3.8-1 failed


Before reporting any errors, please run "fink selfupdate" and try again.


If you continue to have issues, please check to see if the FAQ on Fink's

website solves the problem.  If not, ask on one (not both, please) of

these mailing lists:


The Fink Users List <[email protected]>

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with a carbon copy to the maintainer:


Derek Homeier <[email protected]>


Note that this is preferable to emailing just the maintainer directly,

since most fink package maintainers do not have access to all possible

hardware and software configurations.


Please try to include the complete error message in your report.  This

generally consists of a compiler line starting with e.g. "gcc" or "g++"

followed by the actual error output from the compiler.


Also include the following system information:

Package manager version: 0.45.1

Distribution version: selfupdate-rsync Mon May 25 21:51:19 2020, 10.15, x86_64

Trees: local/main stable/main

Xcode.app: 11.5

Xcode command-line tools: 11.5.0.0.1.1588476445

Max. Fink build jobs:  1

I've tried the following:

make clean
make TARGET=NEHALEM

as suggested in https://github.com/xianyi/OpenBLAS/issues/2227

and then "make install"
Apparently openblas was installed, not in /opt/sw but rather in a /opt/OpenBlas directory. Fink does not recognize its presence and tries to install it again when I run " fink install pymol-py36", ending up with the same failure.

I've changed the installation location in the Makefile.installation for openblas so to install it in /opt/sw  getting the following output


marcopatrone@MBP-di-Marco OpenBLAS-0.3.8 % sudo make install

/Applications/Xcode.app/Contents/Developer/usr/bin/make -j 8 -f Makefile.install install

Generating openblas_config.h in /opt/sw/include

Generating f77blas.h in /opt/sw/include

Generating cblas.h in /opt/sw/include

Copying the static library to /opt/sw/lib

Copying the shared library to /opt/sw/lib

Generating openblas.pc in /opt/sw/lib/pkgconfig

Generating OpenBLASConfig.cmake in /opt/sw/lib/cmake/openblas

Generating OpenBLASConfigVersion.cmake in /opt/sw/lib/cmake/openblas

Install OK!


but still fink doesn't sense its presence and makes again a failing installation of openblas.

What could I do?

Many thanks for your time.
Best,
marco
--
Marco Patrone - PhD
Biocrystallography Unit
Division of Immunology, Transplantation, and Infectious Diseases
DIBIT - Scientific Institute San Raffaele
Via Olgettina 58
20132 Milan
Italy
phone: +39-0226434921
fax: +39-0226434153
URL: http://www.sanraffaele.org/research/degano


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