ATLAS: flush output before os.system()

[jdemeyer]

When doing something like

./sage -i atlas &>my_log_file

the output to my_log_file will be badly ordered because we're not flushing stdout/stderr before calling system() in spkg-install.

New spkg: ​http://boxen.math.washington.edu/home/jdemeyer/spkg/atlas-3.8.4.p2.spkg (for review, changes not yet committed)

atlas-3.8.4.p2 (Jeroen Demeyer, 6 July 2012)

• Trac #13210: Flush stdout and stderr before calling system().
• Detect the Apple linker (which is still unsupported).
• Remove unneeded .orig files in patches/
• Remove mmsearch-with-temp-Solaris-fix.c patch (was needed for gcc-4.4.0 on Solaris).
• Remove copying of patches/*tgz since there are no such files.
• Use 'patch' for patching.

[leif]

AFAIK the "error messages" are suboptimal as well, i.e., at least in some cases exceptions get raised (e.g. KeyError IIRC) and tracebacks printed instead of "Error: <informative text>".

[vbraun]

I think Python tracebacks are more useful than manual error messages, not less. Of course os.system() doesn't raise exceptions so some amount of manual error messages is unavoidable.

[vbraun]

I'd rather keep working on packaging Atlas 3.9.x, any further frobnicating the old package is a waste of time imho.

[jdemeyer]

Replying to vbraun:

I'd rather keep working on packaging Atlas 3.9.x, any further frobnicating the old package is a waste of time imho.

I don't think "I'm working on a new version of feature X" is ever a good excuse to not fix the old feature X.

[jdemeyer]

Diff for the atlas spkg (without deleted files). For reference / review only.

[jdemeyer]

Besides, I think the changes here are likely good for ATLAS-3.9.x also.

Needs review.

[vbraun]

ATLAS-3.9.x is sufficiently different that it requires major changes. The shared library stuff is completely different for starters. I'm happy to apply the changes that still apply in the next version but I'm not going to spend time reviewing this ticket.

[vbraun]

Superseded by #10508