new port: avogadro

[atenderholt@…]

Avogadro is an open source, advanced molecular editor. I believe its inclusion into MacPorts is justified as there are other similar packages such as bkchem, chemtool, openbabel, etc.

Please find attached a Portfile. It installs a working copy of Avogadro into /Applications. Some adjustments may be necessary by someone more familiar with MacPorts.

Adam

[atenderholt@…]

Portfile for science/avogadro

[(none)]

Milestone Port Submissions deleted

[raimue (Rainer Müller)]

This should use the cmake PortGroup which would make it a lot simpler.

[c.herbig@…]

Avogadro is now many versions advanced, and there is a native OS X build. Is it still necessary for a macports inclusion?

[atenderholt@…]

There's probably no reason to include Avogadro in Macports as you pointed out. Feel free to close it.

[cooljeanius (Eric Gallager)]

Replying to c.herbig@…:

Avogadro is now many versions advanced, and there is a native OS X build. Is it still necessary for a macports inclusion?

Well, if someone submitted an updated version of the portfile that builds one of the newer versions, that could be useful for people who like to use MacPorts to manage all their software, and to keep everything linked against MacPorts libraries...

[cooljeanius (Eric Gallager)]

Cc Me!

[c.herbig@…]

I did get this one to work, but I don't know how to fix the following warnings:

--->  Staging avogadro into destroot
Warning: violation by /Applications/Avogadro.app
Warning: avogadro violates the layout of the ports-filesystems!
Warning: Please fix or indicate this misbehavior (if it is intended), it will be an error in future releases!
--->  Installing avogadro @1.1.0_0

Don't get me wrong, I like the idea of even some OS X programs being available here, I was just wondering if anyone even cared since this ticket was so old.

[c.herbig@…]

Newer version

[larryv (Lawrence Velázquez)]

Replying to c.herbig@…:

I did get this one to work, but I don't know how to fix the following warnings:

--->  Staging avogadro into destroot
Warning: violation by /Applications/Avogadro.app
Warning: avogadro violates the layout of the ports-filesystems!
Warning: Please fix or indicate this misbehavior (if it is intended), it will be an error in future releases!
--->  Installing avogadro @1.1.0_0

The build needs to be patched to install the app bundle to ${destroot}${applications_dir}, not /Applications.

[c.herbig@…]

The build needs to be patched to install the app bundle to ${destroot}${applications_dir}, not /Applications.

Might that be something that belongs in the cmake group?

[c.herbig@…]

Also, the status of the port has been changed to closed, wontfix. Shouldn't we open it for this?

[c.herbig@…]

Well, putting this in the portfile didn't work:

configure.pre_args-delete  -DCMAKE_INSTALL_PREFIX=${prefix}
configure.pre_args-append  -DCMAKE_INSTALL_PREFIX=${destroot}${applications_dir}

I don't know what else to do, other than to leave it as a warning.

[c.herbig@…]

removed comments

[c.herbig@…]

Anyway, the portfile does build Avogadro, so unless somebody has a fix for those warnings, it can probably be committed. When those warnings become errors, anybody using it will file it as a bug, and somebody who actually knows what they are doing with this stuff can fix it then.

[larryv (Lawrence Velázquez)]

Replying to c.herbig@…:

Anyway, the portfile does build Avogadro, so unless somebody has a fix for those warnings, it can probably be committed.

No, we should not commit a broken Portfile.

[c.herbig@…]

Cc Me!

[c.herbig@…]

Well, I've already put more time into this than I should have, so if this is an issue, then I'd say on the grounds that Avogadro has a native OS X build, to just forget the port and close the ticket.

[c.herbig@…]

I have been experimenting trying to get Avogadro to install to /Applications/Macports, but I have had no luck. Placing the following into the portfile makes the configure phase acknowledge the correct destroot directory, but when destroot actually happens, it still places it into /Applications.

configure.pre_args  -DCMAKE_INSTALL_PREFIX=${destroot}${applications_dir}/Avogadro.app/Contents

This is the only holdup for committing this port. Unless somebody has a solution to this, I see no reason to keep this ticket/project open since there is already a native mac build on the avogadro site.

[c.herbig@…]

Replying to larryv@…:

Replying to c.herbig@…:

Anyway, the portfile does build Avogadro, so unless somebody has a fix for those warnings, it can probably be committed.

No, we should not commit a broken Portfile.

The developers have informed me that this cannot be changed without their intervention. Meanwhile I am working on a port file for Avogadro2. This ticket can finally be closed as wontfix or (hopefully) superseded by avogadro2.