Bug 339753

Summary:	sci-biology/mothur: fails with forced --as-needed
Product:	Gentoo Linux	Reporter:	Diego Elio Pettenò (RETIRED) <flameeyes>
Component:	New packages	Assignee:	Andrey Kislyuk (RETIRED) <weaver>
Status:	RESOLVED FIXED
Severity:	QA	CC:	sci-biology
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
URL:	http://www.gentoo.org/proj/en/qa/asneeded.xml
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	129413
Attachments:	Build log

Description Diego Elio Pettenò (RETIRED) gentoo-dev

2010-10-04 20:10:56 UTC

I'm reporting this bug because the package in summary fails to build when forcing --as-needed on through spec files (check out http://blog.flameeyes.eu/2008/11/14/problems-and-mitigation-strategies-for-as-needed for details).

Please note that this bug _might_ apply to -Wl,--as-needed in LDFLAGS as well; in both cases it should be fixed. Also, if this is due to the package in question not respecting user-defined LDFLAGS, you should get to fix that too.

Check the attached build log.

Thanks,
Diego

Comment 1 Diego Elio Pettenò (RETIRED) gentoo-dev

2010-10-04 20:11:09 UTC

Created attachment 249584 [details]
Build log

Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev

2010-10-05 08:28:03 UTC

Reported upstream: http://www.mothur.org/forum/viewtopic.php?f=4&t=590

+*mothur-1.13.0-r1 (05 Oct 2010)
+
+  05 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org>
+  -mothur-1.7.2-r1.ebuild, -mothur-1.13.0.ebuild, +mothur-1.13.0-r1.ebuild,
+  +files/mothur-1.13.0-makefile.patch, +files/mothur-1.13.0-overflows.patch:
+  Fix buffer overflows and building with --as-needed wrt bug 339753. Thanks
+  to Diego for the report. Correct dependencies. Drop old.
+