Bug 216619 - biology/bowtie2: fails to build with clang 4.0
Summary: biology/bowtie2: fails to build with clang 4.0
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Jan Beich
URL:
Keywords: needs-patch
Depends on:
Blocks: 216008
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Reported: 2017-01-30 22:24 UTC by Jan Beich
Modified: 2017-02-27 14:10 UTC (History)
1 user (show)

See Also:
bugzilla: maintainer-feedback? (jwb)


Attachments
Unified diff (3.49 KB, patch)
2017-02-20 03:57 UTC, Jason W. Bacon
jwb: maintainer-approval+
Details | Diff

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Description Jan Beich freebsd_committer 2017-01-30 22:24:39 UTC
aligner_result.cpp:1133:10: error: ordered comparison between pointer and zero ('const char *' and 'int')
        if(flag > 0) {
           ~~~~ ^ ~

build log: http://package18.nyi.freebsd.org/data/headamd64PR216008-default/2017-01-29_16h09m05s/logs/errors/bowtie2-2.2.9.log
regressed by: https://github.com/llvm-mirror/clang/commit/4b6ad14285f3
Comment 1 Jason W. Bacon freebsd_committer 2017-02-20 03:57:01 UTC
Created attachment 180156 [details]
Unified diff

Try this patch and let me know if it resolves the error on your end.

I don't see a clang4 port so I'm guessing your using FreeBSD 12 and clang 4 is the base compiler?

I confirmed the new patch with the upstream developer and upgraded to the latest release while I was at it.

It passes poudriere and portlint.
Comment 2 commit-hook freebsd_committer 2017-02-27 14:09:05 UTC
A commit references this bug:

Author: jbeich
Date: Mon Feb 27 14:08:31 UTC 2017
New revision: 434940
URL: https://svnweb.freebsd.org/changeset/ports/434940

Log:
  biology/bowtie2: update to 2.3.0

  - Unbreak with Clang 4.0

  Changes:	https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0
  PR:		216619
  Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)

Changes:
  head/biology/bowtie2/Makefile
  head/biology/bowtie2/distinfo
  head/biology/bowtie2/files/patch-Makefile
  head/biology/bowtie2/files/patch-aligner__result.cpp
Comment 3 Jan Beich freebsd_committer 2017-02-27 14:10:42 UTC
(In reply to Jason Bacon from comment #1)
> Try this patch and let me know if it resolves the error on your end.

Thanks. No more Clang 4.0 issues.

> I don't see a clang4 port so I'm guessing your using FreeBSD 12 and clang 4 is
> the base compiler?

devel/llvm40 has Clang 4.0 but 12.0-CURRENT not yet. I'm using a branch maintained by dim@ until LLVM project tags the release.