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Bug 285220 - [ebuild] sci-chemistry/molden-4.8: version bump
Summary: [ebuild] sci-chemistry/molden-4.8: version bump
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High enhancement
Assignee: Gentoo Chemistry-Related Packages
URL:
Whiteboard:
Keywords: EBUILD
Depends on:
Blocks:
 
Reported: 2009-09-16 16:10 UTC by Michelangelo Scopelliti
Modified: 2010-02-26 05:39 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
proposed ebuild for sci-chemistry/molden-4.8 (molden-4.8.ebuild,1.95 KB, text/plain)
2009-09-16 16:11 UTC, Michelangelo Scopelliti
Details
modified ebuild -- fixes a buffer overflow condition (molden-4.8.ebuild,1.92 KB, text/plain)
2009-09-19 08:37 UTC, Michelangelo Scopelliti
Details

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Description Michelangelo Scopelliti 2009-09-16 16:10:27 UTC
molden 4.8 is out. The proposed ebuild (see attachment) does not rely on fortran.eclass, adds some suggested optimizations, and turns on the mpfit module.

Reproducible: Always

Steps to Reproduce:




This ebuild has been tested only on x86_64 architecture. It should work on other achitectures too, but it should be tested.
Comment 1 Michelangelo Scopelliti 2009-09-16 16:11:20 UTC
Created attachment 204336 [details]
proposed ebuild for sci-chemistry/molden-4.8
Comment 2 Michelangelo Scopelliti 2009-09-19 08:37:01 UTC
Created attachment 204579 [details]
modified ebuild -- fixes a buffer overflow condition

After some testing, I've discovered a problem with any '-O?' option.
This problem happens only when saving a file from Z matrix editor, determining a buffer overflow.
To reproduce:
1) start molden
2) open the Z matrix editor
3) create some content
4) write Z matrix (to a file)
-> buffer overflow detected.

The issue is not present if no -O? options are present.
Curiously, the bug is present in current portage ebuild too.

this new ebuild fixes the issue.
also, since -malign-double is on by default on x86_64 arch, the redundancy has been eliminated.
Comment 3 Markus Dittrich (RETIRED) gentoo-dev 2010-02-26 05:39:02 UTC
Thanks very much for your work and I've just added molden-4.8 
to portage. The actual program abort is triggered by
gcc's FORTIFY_SOURCE and caused by a fairly questionable
strcpy in xwin.c which I've fixed with a patch. 

Since there are other similarly "suspicious" strcpy instances
I'd not be too surprised if more of these FORTIFY_SOURCE
checks will trigger under certain circumstances.

cheers,
Markus