py27-numpy: raise ValueError, "insecure string pickle"

[jowens@…]

OS X 10.11, MacPorts 2.3.4. I'm not quite sure what the error is here, but I believe it's underneath cythonize and is a insecure pickling problem. Googling is surprisingly uninformative. I've had this package installed for quite some time but have not seen this error until this version.

[vincent.liegeois@…]

Cc Me!

[david.alexander.gross@…]

Cc Me!

[elfprince13 (Thomas Dickerson)]

I also have this problem. Has anyone made progress in diagnosing the root cause?

[michaelld (Michael Dickens)]

It looks like the NumPy build in the log is for 1.10.1; the current port version is 1.10.4. Can you try the following (cleaning & updating) and see if it works, and if not post the new error log?

sudo port clean py27-numpy
sudo port selfupdate
sudo port upgrade py27-numpy

Also, which variant(s) are you selecting?

[jowens@…]

It appears I successfully installed this sometime after I filed this bug.

py27-numpy @1.10.4_0+gfortran (active)

[michaelld (Michael Dickens)]

OK; good to know that it's probably something that was fixed since 1.10.1 (in NumPy or elsewhere).

Others have piped up with the same problem. If they could do the clean, selfupdate, upgrade above it would be good to get more feedback before closing out this ticket.

[david.alexander.gross@…]

My journal:

• as a check, installing before trying anything new still failed
• clean cleaned up
• selfupdate self-updated
• numpy upgrade didn't work because it's not installed.
• so I clean and self-updated again for good measure
• upgrade outdated upgraded
• had to uninstall an obsolete something
• trying to install again still didn't work, still an insecure pickle.

I've uploaded my main.log if there's anything there that's useful!

Replying to michaelld@…:

OK; good to know that it's probably something that was fixed since 1.10.1 (in NumPy or elsewhere).

Others have piped up with the same problem. If they could do the clean, selfupdate, upgrade above it would be good to get more feedback before closing out this ticket.

[david.alexander.gross@…]

Still having a problem

[michaelld (Michael Dickens)]

DAG: what variants are you building py27-numpy with here?

[david.alexander.gross@…]

Nothing different than the default on my system:

port variants py27-numpy
py27-numpy has the variants:
   atlas
     * conflicts with Use MacPorts ATLAS Libraries openblas
   clang37: Build using the MacPorts clang 3.7 compiler
     * conflicts with gcc49 gcc5 gcc6 llvm
   gcc49: Build using the MacPorts gcc 4.9 compiler
     * conflicts with clang37 gcc5 gcc6 gfortran llvm
   gcc5: Build using the MacPorts gcc 5 compiler
     * conflicts with clang37 gcc49 gcc6 gfortran llvm
   gcc6: Build using the MacPorts gcc 6 compiler
     * conflicts with clang37 gcc49 gcc5 gfortran llvm
[+]gfortran: Build using the MacPorts gcc 5 Fortran compiler
     * conflicts with gcc49 gcc5 gcc6
   llvm: Build using the Apple native llvm-gcc 4.2 compiler
     * conflicts with clang37 gcc49 gcc5 gcc6
   openblas: Use MacPorts OpenBLAS Libraries
     * conflicts with atlas
   universal: Build for multiple architectures

[michaelld (Michael Dickens)]

OK; good to know. What is the output of the following commands:

port installed and active
uname -a
env
ls /usr/local/bin /usr/local/include /usr/local/lib /Library/Frameworks/

[david.alexander.gross@…]

command output as requested

[michaelld (Michael Dickens)]

Sorry for the long delay; 'trac' does not send me an email when something is attached to a ticket, only when a new comment is made. So, I just saw this now.

You have a ton of stuff installed into /usr/local, by whatever means doesn't matter. Because this is a "standard search path" for most build systems, this stuff will be found and used -- often ahead of stuff in the MacPorts prefix (default /opt/local), and often no matter how hard we specify to the project to use MacPorts stuff (solely, or instead). I -highly- recommend finding ways to get rid of the stuff in /usr/local, maybe replace it with stuff from MacPorts (Tcl / Tk surely; lots of others look familiar too). It is possible that once this stuff is removed you'll need to "uninstall active" and reinstall everything in MacPorts from scratch.

The stuff in /Library/Frameworks looks OK to me.

[david.alexander.gross@…]

No worries, thanks for checking back on this. Thanks for the suggestion--I'll look into what ports are in my /usr/local/ folder that can be replaced.

For this particular ticket, though, it appears my issue is resolved. a clean, an update, and upgrade outdated, and then an install appears to have worked. See new attachment for what updated/upgraded.

Replying to michaelld@…

[david.alexander.gross@…]

Installation appears successful

[michaelld (Michael Dickens)]

Thanks for reporting back. Does anybody else on the ticket have this issue still? Seems like cleaning & updating solve it.