Scientific Applications under Yosemite (Update 12)
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.
I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.
If you do use Homebrew then it is worth updating
brew update brew upgrade
Aabel 3 appears to be working fine
BBEdit version 10.5.13 and newer are compatible with Yosemite
Beaker all seems OK
ChemBioDraw versions 12, 13 and 14 all function as before.
ChemDoodle all seems to work fine
Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.
Conquest and Mercury from CCDC works fine but you may need to reinstall Quartz (see below)
Cytoscape 3.1.1 seems to be working fine
DataWarrior no issues
EndNote X7.2 works well with Yosemite.
Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.
IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK
Igor Pro version 220.127.116.11 works fine
iNMR no problems reported
MacVector 13.0.6 No significant issues reported
Mathematica no issues reported
MOE works fine but you may need to reinstall Quartz (see below)
OpenBabel no issues so far
Opsin all works fine
OSRA no issues
Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.
Pro Fit 6.2 appears to work fine.
Pybel no issues reported
PyCharm works fine
Pymol All these are confirmed to work:
- MacPyMOL 18.104.22.168
- MacPyMOLX11Hybrid 22.214.171.124 after XQuartz reinstall (see below)
- Open-Source PyMOL with homebrew
Known issues with MacPyMOL:
- Movie export broken.
Edu-only-PyMOL (free Student version)
Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports
PyRx 0.8 for docking works fine
RDkit no issues reported
SeeSAR all seems to be working fine
Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.
Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact email@example.com for a temporary alternative license procedure.
Torch no issues
VarSeq no issues
Vortex Upgraded when the developer preview came out. All works fine
The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to firstname.lastname@example.org
VMD no issues reported
Wizard Pro is fully Yosemite compatible
XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"
Updated 30 October 2014