[Bioc-devel] openbabel 2.4.1

[Obenchain, Valerie]

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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>>>
>>
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