Error in Scanning binaries for linking errors

[ahzeeshan (Zeeshan Ahmad)]

On MacOS Catalina, I ran a sudo port selfupdate which gave the following:

--->  Updating MacPorts base sources using rsync
MacPorts base version 2.6.2 installed,
MacPorts base version 2.6.2 downloaded.
--->  Updating the ports tree
--->  MacPorts base is already the latest version

The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated

After running sudo port upgrade outdated, I got the following error:

Nothing to upgrade.
--->  Scanning binaries for linking errors
      [                                        ]  81.4 %[5]    10054 killed     sudo port upgrade outdated

[jmroot (Joshua Root)]

Can you reproduce the error (with e.g. sudo port -d rev-upgrade)? Was there a crash log generated?

[ahzeeshan (Zeeshan Ahmad)]

Cannot reproduce it today.

sudo port upgrade outdated

Nothing to upgrade.
--->  Scanning binaries for linking errors
--->  No broken files found.                             
--->  No broken ports found.

However, my matplotlib was still giving an error while importing (which was the reason I did a sudo port selfupdate in the first place),

>>> import matplotlib.pyplot as plt
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/pyplot.py", line 32, in <module>
    import matplotlib.colorbar
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/colorbar.py", line 27, in <module>
    import matplotlib.artist as martist
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/artist.py", line 13, in <module>
    from .path import Path
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/path.py", line 17, in <module>
    from . import _path, cbook, rcParams
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/_path.cpython-37m-darwin.so, 2): Symbol not found: _MPL_matplotlib__contour_ARRAY_API
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/_path.cpython-37m-darwin.so
  Expected in: flat namespace
 in /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/matplotlib/_path.cpython-37m-darwin.so

So I did a sudo port uninstall py37-pytorch (py37-matplotlib was installed as a dependency of py37-pytorch). When running sudo port install py37-pytorch, I got the error again:

--->  Computing dependencies for py37-pytorch
The following dependencies will be installed: 
 py37-matplotlib
 py37-nltk
 py37-torchtext
Continue? [Y/n]: Y
--->  Fetching archive for py37-matplotlib
--->  Attempting to fetch py37-matplotlib-3.1.3_0+cairo+webagg.darwin_19.x86_64.tbz2 from http://lil.fr.packages.macports.org/py37-matplotlib
--->  Attempting to fetch py37-matplotlib-3.1.3_0+cairo+webagg.darwin_19.x86_64.tbz2 from https://packages.macports.org/py37-matplotlib
--->  Attempting to fetch py37-matplotlib-3.1.3_0+cairo+webagg.darwin_19.x86_64.tbz2 from http://cph.dk.packages.macports.org/py37-matplotlib
--->  Fetching distfiles for py37-matplotlib
--->  Verifying checksums for py37-matplotlib
--->  Extracting py37-matplotlib
--->  Applying patches to py37-matplotlib
Warning: reinplace s|^cairo=False|cairo=True| didn't change anything in /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-matplotlib/py37-matplotlib/work/matplotlib-3.1.3/setup.cfg
--->  Configuring py37-matplotlib
--->  Building py37-matplotlib
--->  Staging py37-matplotlib into destroot
--->  Installing py37-matplotlib @3.1.3_0+cairo+webagg
--->  Activating py37-matplotlib @3.1.3_0+cairo+webagg
--->  Cleaning py37-matplotlib
--->  Fetching archive for py37-nltk
--->  Attempting to fetch py37-nltk-3.4.5_0.darwin_19.noarch.tbz2 from http://lil.fr.packages.macports.org/py37-nltk
--->  Attempting to fetch py37-nltk-3.4.5_0.darwin_19.noarch.tbz2.rmd160 from http://lil.fr.packages.macports.org/py37-nltk
--->  Installing py37-nltk @3.4.5_0
--->  Activating py37-nltk @3.4.5_0
--->  Cleaning py37-nltk
--->  Fetching archive for py37-torchtext
--->  Attempting to fetch py37-torchtext-0.5.0_0.darwin_19.x86_64.tbz2 from http://lil.fr.packages.macports.org/py37-torchtext
--->  Attempting to fetch py37-torchtext-0.5.0_0.darwin_19.x86_64.tbz2.rmd160 from http://lil.fr.packages.macports.org/py37-torchtext
--->  Installing py37-torchtext @0.5.0_0
--->  Activating py37-torchtext @0.5.0_0
--->  Cleaning py37-torchtext
--->  Fetching archive for py37-pytorch
--->  Attempting to fetch py37-pytorch-1.3.1_1+mkl.darwin_19.x86_64.tbz2 from http://lil.fr.packages.macports.org/py37-pytorch
--->  Attempting to fetch py37-pytorch-1.3.1_1+mkl.darwin_19.x86_64.tbz2.rmd160 from http://lil.fr.packages.macports.org/py37-pytorch
--->  Installing py37-pytorch @1.3.1_1+mkl
--->  Activating py37-pytorch @1.3.1_1+mkl
--->  Cleaning py37-pytorch
--->  Updating database of binaries
--->  Scanning binaries for linking errors
      [                                        ]  81.6 %[4]    2968 killed     sudo port install py37-pytorch

I also don’t see any new log generated in /opt/local/var/macports/logs/

Replying to ahzeeshan:

On MacOS Catalina, I ran a sudo port selfupdate which gave the following:

--->  Updating MacPorts base sources using rsync
MacPorts base version 2.6.2 installed,
MacPorts base version 2.6.2 downloaded.
--->  Updating the ports tree
--->  MacPorts base is already the latest version

The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated

After running sudo port upgrade outdated, I got the following error:

Nothing to upgrade.
--->  Scanning binaries for linking errors
      [                                        ]  81.4 %[5]    10054 killed     sudo port upgrade outdated

[jmroot (Joshua Root)]

A crash log would be in /Library/Logs/DiagnosticReports or ~/Library/Logs/DiagnosticReports.

[jmroot (Joshua Root)]

The error importing matplotlib was #60074 by the way.

[ahzeeshan (Zeeshan Ahmad)]

crash-log

[ahzeeshan (Zeeshan Ahmad)]

Just attached the crash log I found in /Library/Logs/DiagnosticReports/. Not sure how helpful it is.

[ryandesign (Ryan Carsten Schmidt)]

So now we know that the crash is in ​our machista library's parse_macho function but we don't know what file libmachista was analyzing when it crashed.

[kencu (Ken)]

odd:

Exception Type: EXC_BAD_ACCESS (Code Signature Invalid)