atlas: add gnutar dependency

[sebastian@…]

On my machine building atlas failed because "gnutar" was not available. I suggest to add the gnutar package to the dependencies.

sudo port install atlas +gcc47
--->  Computing dependencies for atlas
--->  Extracting atlas
Error: org.macports.extract for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port atlas failed

[ryandesign (Ryan Carsten Schmidt)]

Replying to sebastian@…:

On my machine building atlas failed because "gnutar" was not available.

Yes we should add depends_extract-append bin:gnutar:gnutar like we did for php4 recently.

[skymoo (Adam Mercer)]

Cc Me!

[mf2k (Frank Schima)]

This is a different generic issue. #39977.

[mf2k (Frank Schima)]

Apologies. I can confirm this issue and solution on Mavericks.

[jmroot (Joshua Root)]

Please confirm that you built base on Mavericks, as opposed to using a build from some earlier OS version.

[mf2k (Frank Schima)]

@jmr: I can confirm I am using macports from the latest trunk.

$ svn up
Updating '.':
U    src/macports1.0/macports.tcl
U    ChangeLog
Updated to revision 112484.

$ make clean
===> making clean in doc
rm -f *.{1,5,7}.gz
===> making clean in src
...
make[1]: Nothing to be done for `clean'.

$ ./configure 
checking build system type... x86_64-apple-darwin13.0.0
checking host system type... x86_64-apple-darwin13.0.0
checking target system type... x86_64-apple-darwin13.0.0
checking MacPorts version... 2.2.99
checking for sw_vers... /usr/bin/sw_vers
checking for defaults... /usr/bin/defaults
checking for xcode-select... /usr/bin/xcode-select
checking Mac OS X version... 10.9
checking Xcode location... /Applications/Xcode.app/Contents/Developer
checking Xcode version... 5.0.1
...

$ make
===> making all in doc
...

$ sudo make install
===> making install in doc
...
$ port version
Version: 2.2.99
$ port installed atlas
The following ports are currently installed:
  atlas @3.10.1_5+gcc48 (active)
$ sudo port uninstall gnutar
--->  Deactivating gnutar @1.26_0
--->  Cleaning gnutar
--->  Uninstalling gnutar @1.26_0
--->  Cleaning gnutar
$ sudo port uninstall atlas
--->  Deactivating atlas @3.10.1_5+gcc48
--->  Cleaning atlas
--->  Uninstalling atlas @3.10.1_5+gcc48
--->  Cleaning atlas
$ sudo port install atlas
--->  Computing dependencies for atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas
--->  Fetching distfiles for atlas
--->  Verifying checksums for atlas
--->  Extracting atlas
Error: org.macports.extract for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_mports_trunk_dports_math_atlas/atlas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port atlas failed

[sebastian@…]

I second that. Problem is still present (using 2.2.99). The atlas portfile calls "gnutar" explicitly and there is no gnutar on my 10.9 install.

[jmroot (Joshua Root)]

Yeah, I now see that it has a custom extract phase. If bsdtar works too it could just call "tar" instead of "gnutar".

[ryandesign (Ryan Carsten Schmidt)]

I have a patch to fix this; I'm testing it now. I've rewritten the port to not override the standard extract phase. However, it seems gnutar is required; bsdtar experiences errors extracting this tarball.

[ryandesign (Ryan Carsten Schmidt)]

proposed patch

[sebastian@…]

I also played around with bsdtar but it seems like one cannot convince it to disregard some strange file ownerships. However, your patch works for me (10.9) - I guess it's more elegant than adding another dependency :)

[ryandesign (Ryan Carsten Schmidt)]

Oh I do add a dependency. It's just a bit hidden amongst other cleanup of the portfile.

It's not a file ownership issue; it's just a messed-up archive. ​This bug report explains what's wrong with the atlas-3.10.1 archive, and also suggests a flag we can use to let bsd tar extract it ("-k").

[ryandesign (Ryan Carsten Schmidt)]

​The developer has been made aware of the problem and found a solution which is in the 3.11 development branch and may be backported to the 3.10 branch.

Meanwhile here's a new patch to allow extract to succeed with BSD tar.

[ryandesign (Ryan Carsten Schmidt)]

proposed patch

[sebastian@…]

Even better; second patch work too. Thanks!

[ryandesign (Ryan Carsten Schmidt)]

r112566