cantera binary files not executable

[jjstickel (Jonathan Stickel)]

With the recent version update to cantera (2.2.0), some of the binary files are not installed as executable. The attached patch resolves this. I did not test with the devel subport.

Also, I found the macports-archived source file to be stale, and the one direct from ​https://github.com/Cantera/cantera/releases/download/v2.2.0/cantera-2.2.0.tar.gz needed different checksums.

[ryandesign (Ryan Carsten Schmidt)]

Replying to jjstickel@…:

With the recent version update to cantera (2.2.0), some of the binary files are not installed as executable. The attached patch resolves this. I did not test with the devel subport.

The file attributes proc should be used instead of using system to call chmod.

Also, I found the macports-archived source file to be stale, and the one direct from ​https://github.com/Cantera/cantera/releases/download/v2.2.0/cantera-2.2.0.tar.gz needed different checksums.

I do not experience a checksum error with the port as it is currently written, but I would experience one if I applied your patch. The port currently uses "tarball" style download, whereas the URL you show above is a "release" style download, and yes, it is normal that these would have different checksums and slightly different contents. The former is automatically generated from the repository by the github architecture, whereas the second is manually created by the developers and uploaded to github.

It is true that the port should be updated to use the "release" style download (by using github.tarball_from releases), but unless this improves the build of the software in some way, it can wait until the next version update.

If switching to "release" would improve the build, then the stealth update recipe must be followed.

[macports@…]

Sorry, that was a bit too early from my side (Original text: I wasn't able to reproduce your error on my system: Both ck2cti and ctml_writer are executable. The script setup_cantera is not needed as all files are installed into standard directories.)

You're right, /opt/local/bin/ck2cti and the other Cantera binaries in that directory are not installed as executables. However, the ones installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ are installed as executables.

I assume that it would either be good to have all files executable, or to just have one binary in the first place. Is there a recommended way of doing this?

The reason github.tarball_from releases is not used is because this would result in failures in the cantera-devel subport.

[larryv (Lawrence Velázquez)]

Replying to ryandesign@…:

It is true that the port should be updated to use the "release" style download (by using github.tarball_from releases), but unless this improves the build of the software in some way, it can wait until the next version update.

I removed github.tarball_from releases in r137350 because the tarball did not seem to differ from the release, and leaving it in would have complicated things with the cantera-devel subport (r137351), which must fetch a tarball.

[jjstickel (Jonathan Stickel)]

Replying to ryandesign@…:

Replying to jjstickel@…:

With the recent version update to cantera (2.2.0), some of the binary files are not installed as executable. The attached patch resolves this. I did not test with the devel subport.

The file attributes proc should be used instead of using system to call chmod.

OK; can you point me to an example? I looked through the Macports documentation but couldn't find anything. I know that "system" calls are not preferred.

I was just pointing out the inconsistencies of the tarballs and checksums. That's fine if there is a good reason for the way things are.

[larryv (Lawrence Velázquez)]

Replying to jjstickel@…:

OK; can you point me to an example? I looked through the Macports documentation but couldn't find anything. I know that "system" calls are not preferred.

file attributes is a Tcl command, not part of MacPorts.

• ​http://www.tcl.tk/man/tcl8.5/TclCmd/file.htm#M6
• ​http://wiki.tcl.tk/10066

[jjstickel (Jonathan Stickel)]

using "file attributes"

[jjstickel (Jonathan Stickel)]

I updated the portfile patch to use "file attributes" and removed the change to the checksums.

[macports@…]

Thank you for the patch!

If it is standard procedure to have binaries both in /opt/local/bin and in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/, this patch should be applied.

[larryv (Lawrence Velázquez)]

Replying to macports@…:

You're right, /opt/local/bin/ck2cti and the other Cantera binaries in that directory are not installed as executables. However, the ones installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ are installed as executables.

Are the files in the main bin directory distinct from the ones under the Python framework?

[macports@…]

Replying to larryv@…:

Are the files in the main bin directory distinct from the ones under the Python framework?

Well, in fact, they are. While the ones in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ rely on functions of the Python Cantera module, the ones in /opt/local/bin/ restate the entire code in Python. The latter is used if the Python module is not installed (however, Python is needed anyway to run the script). Using the above Portfile, the Python module is always installed, so it doesn't make a difference.

Still, it is probably best to apply jjstickel's patch as is. There are numerous other Portfiles installing binaries both in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ and /opt/local/bin.

[ryandesign (Ryan Carsten Schmidt)]

Replying to macports@…:

There are numerous other Portfiles installing binaries both in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ and /opt/local/bin.

Are there really? All of the ones I can remember only install symlinks in /opt/local/bin pointing to the ones in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin.

[ryandesign (Ryan Carsten Schmidt)]

Replying to macports@…:

The reason github.tarball_from releases is not used is because this would result in failures in the cantera-devel subport.

Not if you only include the directive conditionally where it's needed, e.g.

if {${subport} eq ${name}} {
    github.tarball_from releases
    checksums ...
}

[macports@…]

Replying to ryandesign@…:

Replying to macports@…:

There are numerous other Portfiles installing binaries both in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ and /opt/local/bin.

Are there really? All of the ones I can remember only install symlinks in /opt/local/bin pointing to the ones in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin.

You're right, I couldn't find one that isn't a symlink.

[kurthindenburg (Kurt Hindenburg)]

Cc Me!

[kurthindenburg (Kurt Hindenburg)]

It looks like these are not executable

-rw-r--r--  1 macports  admin  82752 Jun  4  2015 /opt/local/bin/ck2cti
-rw-r--r--  1 macports  admin  88274 Jun  4  2015 /opt/local/bin/ctml_writer
-rw-r--r--  1 macports  admin   1966 Jan 19 23:07 /opt/local/bin/setup_cantera

[jjstickel (Jonathan Stickel)]

Replying to khindenburg@…:

It looks like these are not executable

-rw-r--r--  1 macports  admin  82752 Jun  4  2015 /opt/local/bin/ck2cti
-rw-r--r--  1 macports  admin  88274 Jun  4  2015 /opt/local/bin/ctml_writer
-rw-r--r--  1 macports  admin   1966 Jan 19 23:07 /opt/local/bin/setup_cantera

The patch attached to this ticket will solve this problem. The maintainers got hung up on a technical detail and haven't committed it.

[kurthindenburg (Kurt Hindenburg)]

done r144963