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schrodinger / coordgenlibs

Schrodinger-developed 2D Coordinate Generation
BSD 3-Clause "New" or "Revised" License
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errors using v3.0.0 with the RDKit master #104

Closed greglandrum closed 2 years ago

greglandrum commented 3 years ago

I just tried building the RDKit master against v3.0.0 and things don't look good.

Everything compiles without complaint, but when running the RDKit tests I encounter problems.

Here's what I get for a standard release build:

(base) glandrum@Badger:/scratch/RDKit_git/build$ ./External/CoordGen/testCoordGen 
[10:04:36] -------------------------------------
[10:04:36] test2: using templates
*** stack smashing detected ***: terminated
Aborted (core dumped)

That's an awesome runtime error (and one I hadn't seen before), but it's probably not intended behavior. ;-)

When built in debug mode that particular test passes, but then I get a seg fault in the test which attempts to use the minimizeOnly mode (the seg fault itself is at this line: https://github.com/rdkit/rdkit/blob/master/External/CoordGen/CoordGen.h#L226). I guess it's probably expected that we'd need to update this on the RDKit side, but it doesn't seem like I should be able to trigger a seg fault like this.

greglandrum commented 3 years ago

It may be that the "stack smashing" problem was me having a screwed up build environment. I will try this again later today

ricrogz commented 2 years ago

Ugh, I hit this yesterday. I have spent some time trying to figure out what was going on, and in the end, it just went away after cleaning up old instances of maeparser & coordgenlibs (v.2.0.3) that had been downloaded to rdkit's External/Coordgen dir.

Since I discovered that, I have been able to consistently reproduce and fix the issue by putting the sources back and removing them again.

greglandrum commented 2 years ago

This has been resolved