Scientific Applications under Sierra (Update 14)
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. I’ll update the list regularly and feel free to send in information.
4Peaks no reported issues
Avogadro all seems OK
BBEdit version 11.6.2 and newer are compatible, recommend against using earlier versions
Brainsight requires version 2.3.3 for full compatibility with 10.12 Sierra. You could note too that 2.0 through 2.2.x will never work because 10.12 removed support for garbage collected applications. 2.3.x uses ARC
ChemDraw the official line is that it is not supported, even under El Capitan there were reports of copy/paste issues. One user reports “ChemDraw 15 is working fine for me. copy/paste, everything without issues”.
ChemDoodle no reported issues
CrystalMaker “We are pleased to confirm that all our latest software runs fine on macOS “Sierra”, as well as OS X 10.11 “El Capitan”, 10.10 “Yosemite”, and earlier.”
CYLview app launcher (icon on the desktop or the dock) does not work need to start using “Terminal”
DataDesk Data Desk 8 for Mac runs on OS X 10.7 up to 10.12
DataWarrior requires Java installation
EndNote From Endnote (Thomson Reuters) version 7: Message for Mac user planning to update to Sierra: In preparation for Apple's release of macOS Sierra on September 20, we have been testing various versions of EndNote. Through our testing, we discovered some issues with the EndNote PDF viewer. These issues have been reported to Apple, but in the meantime, we recommend that you DO NOT upgrade to macOS Sierra.
EnzymeX no reported issues
Evernote a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this.
Findings no reported issues
Fortran users will be happy to hear there are no reported issues with FTranProjectBuilder
GAMESS no reported issues.
Homebrew, after every update it is worth checking your homebrew installation.
Username$ brew doctor Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry and just ignore them. Thanks! Warning: /usr/local is not writable. You should probably change the ownership and permissions of /usr/local back to your user account. sudo chown -R $(whoami) /usr/local Warning: /usr/local is not writable. Even if this directory was writable when you installed Homebrew, other software may change permissions on this directory. For example, upgrading to OS X El Capitan has been known to do this. Some versions of the "InstantOn" component of Airfoil or running Cocktail cleanup/optimizations are known to do this as well. You should probably change the ownership and permissions of /usr/local back to your user account. sudo chown -R $(whoami) /usr/local
Once corrected you can then type
brew update brew upgrade
You may get this error
$brew update /usr/local/Library/brew.sh: line 32: /usr/local/Library/ENV/scm/git: No such file or directory
simply retyping brew update seems to resolve the issue
If you have previously installed Openbabel using
brew install mcs07/cheminformatics/open-babel --HEAD
The "--HEAD" part means install the latest development version from GitHub. The latest version of OpenBabel is now available so type
brew uninstall mcs07/cheminformatics/open-babel Uninstalling /usr/local/Cellar/open-babel/HEAD... (309 files, 14.6M) brew install mcs07/cheminformatics/open-babel You can check you have the latest version installed by type this in a Terminal window obabel -V Open Babel 2.4.0 -- Sep 24 2016 -- 14:01:18
iBabel seems to work fine with the latest version of OpenBabel under Sierra. One advantage to updating to OpenBabel 2.4.0 is that previews now work with Quicklook.
iPython Notebook all working fine
Lego Mindstorms At the moment everything seems to be running really great on Sierra. However, please let you readers know they are welcome to contact us via the website way you did if they run into any errors. We'd be happy to solve them!
Manuscripts no reported issues
Mathematica 11.0.1 has been compatibility tested with macOS Sierra and you should not run into any OS-specific compatibility issues. The font-panel is disabled, but we are actively working to address this as soon as possible.
Mendeley no issues reported
MOE working fine, XQuartz did not need reinstalling. However the MOE app launcher (icon on the desktop or the dock) does not work because Apple changed some fundamental system components which affects lots of programs not specifically compiled for the newest MacOSXs. Also you cannot double click on a file to open it in MOE. You can still start MOE from the command line
It then works perfectly. Update, just had an email from CCG support, The problem with the MOE app launcher on MacOSX Sierra has been fixed in the MOE 2016 release.
MOPAC all seems to be working fine.
osra crashed with error abort trap: 6. I uninstalled using brew then reinstalled
brew uninstall osra Uninstalling /usr/local/Cellar/osra/2.0.1... (7 files, 1.6M) brew install osra
Then worked fine
Pandoc depends on llvm-3.5, not supported on Sierra. Llvm-3.9 is supported, installation using Homebrew seems to be OK.
Papers Mac 3.4.7 (527) is now available! Fixes a couple of problems under Sierra. A crash that can occur when switching PDFs, The search in PDF functionality is restored
R latest version (3.3.1) all seems fine
rdkit installed using home-brew works fine.
Readcube Version 2.22.13732 is Mac OS Sierra (v10.12) compatibility update.
Scansnap Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank. Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder] Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.
Schrodinger a reader sent in this response. We received your query regarding MacOS Sierra. Unfortunately our current, 2016-3 release, do not yet support MacOS Sierra but we have plans to include support for this OS for the upcoming 2016-4 release of our software.
SeeSAR version 5.3 now, 5.4 will come out shortly. No compatibility issues observed/reported.
Studies no reported issues
UCSF Chimera version 1.11.1 seems to be working fine
Wizard worked great with the developer pre-releases, no reported issues
Vortex no problems so far, the embedded chemical drawing app Elemental appears to have no issues.
XQuartz did not require reinstallation :-) however there are reports of an intermittent display not found error when launching apps from a Linux box.
Allow applications downloaded from anywhere in macOS Sierra, if you open the security panel in the Settings the default options in Sierra are as shown below. There is no longer the option to open applications from Anywhere.
Apple have removed this function on macOS Sierra, but you can re-enable it running this in terminal
sudo spctl --master-disable
You can restore it back to the default setting using
sudo spctl --master-enable
I’ll add more updates later.