#360 LoadFormatFiles error for *format.so in OSX binary 2.1.1

[Evan Ingersoll]

I've just installed the mac binary version 2.1.1, and so far all attempts to run the program generate a set of LoadFormatFiles errors. I've tried several files, going from cml to pdb or pdb to cml, and I've tried both direct command-line invocation and running via iBabel. This might be an installer problem, a system config problem, or simple user error.

os version: osX 10.4.11
python version: 2.3.5
babel version: 2.1.1 via mac binary installer pkg

typical error message (this one from iBabel, but command-line is the same)

computer:~ me$ /usr/local/bin/babel -icml '/Users/me/Documents/web_downloads/1UD0.pdb' -ocml '/Users/me/Desktop/outputfile.cml'

*** Open Babel Error in LoadFormatFiles
/usr/local/lib/openbabel/cdxmlformat.so did not load properly
==============================
*** Open Babel Error in LoadFormatFiles
/usr/local/lib/openbabel/cmlformat.so did not load properly
==============================
*** Open Babel Error in LoadFormatFiles
/usr/local/lib/openbabel/cmlreactlformat.so did not load properly
==============================
*** Open Babel Error in LoadFormatFiles
/usr/local/lib/openbabel/pubchem.so did not load properly
==============================
*** Open Babel Error in LoadFormatFiles
/usr/local/lib/openbabel/xmlformat.so did not load properly
babel: cannot read input format!

Am attaching a typical pdb file that fails to convert.

[Evan Ingersoll]

a test pdb file that fails to convert to cml, zipped to fit

[Noel O'Boyle]

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Does conversion from PDB to MOL2 work okay? If so, then the problem is only with the XML formats such as CML. Is libxml installed on your system? (I am not familiar with MacOSX so I cannot help with the specifics)

[Evan Ingersoll]

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Conversion from PDB to MOL2 appears to work -- the same *format.so errors appear, but I also get a nice output file. A quick look suggests that OSX is supposed to come with libxml and libxslt installed. I don't, however, find them in /usr/lib where my xml2Conf suggests they should be. I also note that I have Maya installed on this system, with leftover directories that suggest it installed libxml2 somewhere. I'll see if re-installing libxml does the trick.

Thanks,
Evan

[Evan Ingersoll]

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Semi-resolved: this is an intel-vs-ppc issue. I've tried updating/re-installing libxml2 on my intel laptop, no change in symptoms. However, my older PPC mac has no trouble converting cml files and produces no errors. Is it possible the whole issue is that the .so files in question are ppc-only binaries?

Thanks,
Evan

[Geoff Hutchison]

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It's possible, although somewhat unlikely that it's a PPC-only binary. However, the binaries were compiled on PowerPC under Tiger. I'm not sure if libxml2 was Universal on Tiger PPC systems.

I will upload a binary package of 2.2.0b5 snapshot which should be completely universal. If you'd like to try that out, I would greatly appreciate knowing if it solves the problem.

[Geoff Hutchison]

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There is now a Mac binary for 2.2.0b6. Please try this -- if it does not work, please post a comment here. Otherwise I'm marking this bug as fixed, "Pending" any clarification from you.

[Fredrik]

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I had the same problem on a MacBook with 10.5.3 on it. The 2.2.0b6 binary solved the problem for me. (By the way, the installer said that it was 2.2.0b5 when showing credits...)

/Fredrik

[Evan Ingersoll]

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2.2.0b6 seems to have fixed this for me. It now works fine from command line, anyway, which it didn't before.
Thanks!
Evan