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Bug 725300

Summary: sci-biology/abyss calls ar directly
Product: Gentoo Linux Reporter: Agostino Sarubbo <ago>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: RESOLVED FIXED    
Severity: normal CC: haskell
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
URL: https://github.com/bcgsc/abyss/pull/335
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 243502    
Attachments: build.log

Description Agostino Sarubbo gentoo-dev 2020-05-25 10:12:16 UTC
This is an auto-filed bug because sci-biology/abyss calls ar directly.
The issue was originally discovered on amd64, but it may be reproducible on other arches as well.
If you think that a different summary clarifies the issue better, feel free to change it.
Attached build log and emerge --info.

NOTE:
If you think it doesn't make sense fix these type of issues, I'd like to point out that won't be possible use a different AR implementation (like llvm-ar) by setting the AR variable. So this issue has been reproduced by setting the AR variable to x86_64-pc-linux-gnu-ar and by removing the /usr/bin/ar binary.
Comment 1 Agostino Sarubbo gentoo-dev 2020-05-25 10:12:22 UTC
Created attachment 641704 [details]
build.log

build log and emerge --info
Comment 2 Sergei Trofimovich gentoo-dev 2020-05-25 10:44:51 UTC
I think I broke it when bumped to 2.0.3 and dropped AR patch. Looking.
Comment 3 Larry the Git Cow gentoo-dev 2020-05-25 10:56:25 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=363526d4663d10660c2c593d11a9ab3707443572

commit 363526d4663d10660c2c593d11a9ab3707443572
Author:     Sergei Trofimovich <slyfox@gentoo.org>
AuthorDate: 2020-05-25 10:51:11 +0000
Commit:     Sergei Trofimovich <slyfox@gentoo.org>
CommitDate: 2020-05-25 10:51:11 +0000

    sci-biology/abyss: respect AR override, bug #725300
    
    Use AM_PROG_AR to default to standard AR discovery
    instead of make's 'ar'.
    
    Reported-by: Agostino Sarubbo
    Closes: https://bugs.gentoo.org/725300
    Package-Manager: Portage-2.3.100, Repoman-2.3.22
    Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>

 sci-biology/abyss/abyss-2.0.3-r1.ebuild           | 56 +++++++++++++++++++++++
 sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 +++++
 2 files changed, 67 insertions(+)
Comment 4 Sergei Trofimovich gentoo-dev 2020-05-25 11:01:30 UTC
Proposed fix upstream as https://github.com/bcgsc/abyss/pull/335