Bug 260389 - biology/bowtie: update to 1.3.1
Summary: biology/bowtie: update to 1.3.1
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: Jason W. Bacon
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-12-13 15:30 UTC by Piotr Kubaj
Modified: 2021-12-14 01:50 UTC (History)
1 user (show)

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

Attachments
patch (6.01 KB, patch)
2021-12-13 15:30 UTC, Piotr Kubaj 		pkubaj: maintainer-approval? (jwb)
 Details | Diff
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Description Piotr Kubaj freebsd_committer freebsd_triage 2021-12-13 15:30:13 UTC 
Created attachment 230078 [details]
patch

- fixes build on powerpc64 and powerpc64le (probably also aarch64 and maybe riscv64, but untested),
- move to USES=compiler:gcc-c++11-lib to link to libc++,
- all the patches are now not necessary
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2021-12-13 21:01:14 UTC 
Thanks for the update.

I fixed build on aarch64 simply by amending the popcnt check.

GCC seems unnecessary.  It builds fine for me with base clang on 13.0 aarch64,amd64,powerpc64 and on 12.2 amd64.  Is the gcc-c++11-lib for 12.x ppc64?  If so, is it really needed or might c++11-lib suffice?
Comment 2 Piotr Kubaj freebsd_committer freebsd_triage 2021-12-13 22:49:49 UTC 
Well, the current version in ports uses GCC, I didn't change that. Regarding 12 on powerpc64, anyone using should really move to 13 :)
Comment 3 Jason W. Bacon freebsd_committer freebsd_triage 2021-12-14 01:05:30 UTC 
I agree.  I'll throw in c++11-lib just in case since it might prevent a package build failure.
Comment 4 commit-hook freebsd_committer freebsd_triage 2021-12-14 01:44:17 UTC 
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=eb67c2b94c0b5846d825da791060e0b4c72fc248

commit eb67c2b94c0b5846d825da791060e0b4c72fc248
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2021-12-14 01:41:19 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2021-12-14 01:43:44 +0000

    biology/bowtie: Update to 1.3.1

    Also adds support for aarch64 and powerpc64*

    Changes:        https://github.com/BenLangmead/bowtie/tags

    PR:             260389
    Reported by:    pkubaj

 biology/bowtie/Makefile                            | 22 ++++----
 biology/bowtie/distinfo                            |  5 +-
 biology/bowtie/files/patch-Makefile                | 60 +++++-----------------
 biology/bowtie/files/patch-ebwt.h (gone)           | 11 ----
 .../bowtie/files/patch-processor__support.h (gone) | 11 ----
 biology/bowtie/pkg-plist                           |  5 +-
 6 files changed, 34 insertions(+), 80 deletions(-)
Comment 5 Jason W. Bacon freebsd_committer freebsd_triage 2021-12-14 01:50:44 UTC 
Committed with changes to add aarch64 support, remove GCC dep, and respect ports CXXFLAGS.

Thanks!