Bug 259627 - biology/freebayes: update to 1.3.5
Summary: biology/freebayes: update to 1.3.5
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: 2021-11-03 11:57 UTC by Piotr Kubaj
Modified: 2021-11-03 20:55 UTC (History)
1 user (show)

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


Attachments
patch (8.45 KB, patch)
2021-11-03 11:57 UTC, Piotr Kubaj
no flags Details | Diff
v2 (16.58 KB, patch)
2021-11-03 15:22 UTC, Piotr Kubaj
no flags Details | Diff
v3 (8.38 KB, patch)
2021-11-03 18:05 UTC, Piotr Kubaj
no flags Details | Diff
v4 (16.58 KB, patch)
2021-11-03 18:13 UTC, Piotr Kubaj
pkubaj: maintainer-approval? (jwb)
Details | Diff

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Description Piotr Kubaj freebsd_committer freebsd_triage 2021-11-03 11:57:35 UTC
Created attachment 229241 [details]
patch

This version builds fine on powerpc64le, probably also on arm*.

-msse2 is not necessary on i386.
MAKE_JOBS_UNSAFE is probably not necessary, builds fine with -j32.
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2021-11-03 13:56:54 UTC
Fetch fails:

=> Attempting to fetch https://codeload.github.com/ekg/intervaltree/tar.gz/b90527f?dummy=/ekg-intervaltree-b90527f_GH0.tar.gz
fetch: 72540: No such file or directory
fetch: https://codeload.github.com/ekg/intervaltree/tar.gz/b90527f?dummy=/ekg-intervaltree-b90527f_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/ekg/intervaltree/tar.gz/b90527f?dummy=/ekg-intervaltree-b90527f_GH0.tar.gz: size of remote file is not known
ekg-intervaltree-b90527f_GH0.tar.gz                     70 kB  950 kBps    00s
=> Attempting to fetch http://distcache.FreeBSD.org/ports-distfiles/ekg-intervaltree-b90527f_GH0.tar.gz
fetch: 72540: No such file or directory
fetch: http://distcache.FreeBSD.org/ports-distfiles/ekg-intervaltree-b90527f_GH0.tar.gz: Not Found
=> Couldn't fetch it - please try to retrieve this
=> port manually into /usr/ports/distfiles/ and try again.
*** Error code 1

Stop.
make: stopped in /usr/ports/wip/freebayes
Comment 2 Piotr Kubaj freebsd_committer freebsd_triage 2021-11-03 15:22:42 UTC
Created attachment 229245 [details]
v2

Corrected GH_TUPLES and patches from files were mostly removed.
Comment 3 Piotr Kubaj freebsd_committer freebsd_triage 2021-11-03 18:05:34 UTC
Created attachment 229250 [details]
v3

-msse2 is not necessary anymore for i386.
Comment 4 Piotr Kubaj freebsd_committer freebsd_triage 2021-11-03 18:13:47 UTC
Created attachment 229251 [details]
v4

Sorry, I sent a patch for vcflib instead.
Comment 5 commit-hook freebsd_committer freebsd_triage 2021-11-03 20:54:41 UTC
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=dc64b13129b889531be2dae60218484f9444cf92

commit dc64b13129b889531be2dae60218484f9444cf92
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2021-11-03 20:49:05 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2021-11-03 20:49:05 +0000

    biology/freebayes: Update to 1.3.5

    Fixes build on powerpc64 and aarch64, possibly others.

    Changes:        https://github.com/freebayes/freebayes/tags

    PR:             259627
    Reported by:    pkubaj

 biology/freebayes/Makefile                         | 53 +++++++++---------
 biology/freebayes/distinfo                         | 60 ++++++++++-----------
 biology/freebayes/files/patch-Makefile (gone)      | 20 -------
 .../files/patch-SeqLib_bwa_Makefile (gone)         | 14 -----
 .../files/patch-SeqLib_bwa_bwt__lite.c (gone)      | 10 ----
 .../files/patch-SeqLib_bwa_bwtgap.h (gone)         | 10 ----
 .../files/patch-SeqLib_bwa_kthread.c (gone)        | 10 ----
 .../freebayes/files/patch-SeqLib_bwa_rle.h (gone)  | 11 ----
 .../files/patch-SeqLib_fermi-lite_Makefile (gone)  | 12 -----
 .../files/patch-SeqLib_fermi-lite_rle.h (gone)     | 11 ----
 .../files/patch-SeqLib_htslib_Makefile (gone)      | 38 -------------
 biology/freebayes/files/patch-src_Makefile (gone)  | 62 ----------------------
 .../freebayes/files/patch-vcflib_Makefile (gone)   | 13 -----
 13 files changed, 53 insertions(+), 271 deletions(-)
Comment 6 Jason W. Bacon freebsd_committer freebsd_triage 2021-11-03 20:55:30 UTC
Thanks!