[Bioc-devel] openbabel 2.4.1
Hi, I've updated to 2.4.1 on veracruz1. ChemmineOB did not install clean - you'll see the errors on tomorrow's build report (May 26). As I mentioned, updating to 2.4.1 on Linux will be a hassle for the Linux users. Because 2.4.1 is not available with apt-get Open Babel must be installed from source. I would recommend keeping 2.3.0 on Linux and Windows and 2.4.1 on Mac. This is beneficial all around - Mac users can use 'brew install' and Linux users use 'apt-get install'. Windows users have to install from source regardless of version so you might as well stick with what they already have. Having the 2 Open Babel versions on the build machines also serves as a double check that future developments on ChemmineOB are backwards compatible. If you feel strongly about having 2.4.1 on Linux, please update ChemmineOB/INSTALL with the steps required to manually install 2.4.1 from source on Linux. Valerie
On 05/24/2017 12:48 PM, Kevin Horan wrote:
Valerie,
Sorry for the confusion. I've tested ChemmineOB on mac and Linux
with the new openbabel 2.4.1 and got them both working. The Linux
version does not require any changes, and the mac version may just
require some compiler flag changes. I figured I'd let you install it and
then see what specific errors were produced before uploading a changed
version. I've not yet tested in on windows though, but since it works
unchanged on linux, and the mac version compiler flags are only related
to the use of libc++/libstdc++, I think it should work fine on windows too.
Kevin
On 05/24/2017 06:59 AM, Obenchain, Valerie wrote:
Kevin, It looks like ChemmineOB has not changed in the devel branch since the release - still at version 1.15.0. Herve installed OpenBabel 2.4 on the Macs a couple of months ago but it was not compatible with the ChemmineOB version at the time. Because of this he had to install OpenBabel 2.3. I've looked in the svn logs and don't see any record of 'now compatible' or 'tested with' 2.4. so I'm not sure why you think ChemmineOB would now be compatible with 2.4. Using OpenBabel 2.4 would be good for Mac users because that's the version you get with 'brew install openbabel'. This change, however, is not a good thing for linux users because with 'apt-get install libopenbable-dev' you get version 2.3 and not 2.4. Updating on windows is a similar install from source situation. Please explain what testing you've done to ensure the package is compatible with OpenBabel 2.4. I'm also not sure why you want 2.4 on the build machines if ChemmineOB is backwards compatible with 2.3. Is there new functionality? Valerie On 05/22/2017 01:21 PM, Kevin Horan wrote:
The package ChemmineOB depends on the external library OpenBabel. There is now a new version of it, version 2.4.1. Could you please install this on all three operating systems (just for devel )? You can find general OpenBabel build instructions here <http://openbabel.org/wiki/Install_%28source_code%29>, and ChemmineOB specific instructions in the INSTALL file. On the mac, it should work with libc++ now (previously it only worked with libstdc++), so don't force it use libstd++ anymore (unless you have other reasons for doing so, in which case just let me know so I can adjust the make file). No special CMAKE flags should be necessary. Thanks. Kevin [[alternative HTML version deleted]]
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