Bug 245240 - biology/kallisto: fix build on GCC architectures
Summary: biology/kallisto: fix build on GCC architectures
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: 2020-04-01 16:23 UTC by Piotr Kubaj
Modified: 2020-04-02 13:42 UTC (History)
1 user (show)

See Also:
bugzilla: maintainer-feedback? (jwb)
pkubaj: merge-quarterly?

Attachments
patch (779 bytes, patch)
2020-04-01 16:24 UTC, Piotr Kubaj 		pkubaj: maintainer-approval? (jwb)
 Details | Diff
View All Add an attachment (proposed patch, testcase, etc.)

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Description Piotr Kubaj freebsd_committer freebsd_triage 2020-04-01 16:23:25 UTC 
kallisto 0.46.2 fails to build with GCC:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/Bootstrap.cpp:1:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/Bootstrap.h:57:106: error: 'uint' has not been declared
   57 |       const std::vector<int>& fld, const std::vector<int>& preBias, const std::vector<double>& postBias, uint compression, size_t index_version,
      |                                                                                                          ^~~~


Including sys/types.h is necessary.
Please MFH after commit since new quarterly is imminent.
Comment 1 Piotr Kubaj freebsd_committer freebsd_triage 2020-04-01 16:24:45 UTC 
Created attachment 212932 [details]
patch
Comment 2 commit-hook freebsd_committer freebsd_triage 2020-04-01 23:46:21 UTC 
A commit references this bug:

Author: jwb
Date: Wed Apr  1 23:35:39 UTC 2020
New revision: 530250
URL: https://svnweb.freebsd.org/changeset/ports/530250

Log:
  kallisto: Patch for build with GCC

  PR:             ports/245240
  Submitted by:   pkubaj

Changes:
  head/biology/kallisto/Makefile
  head/biology/kallisto/files/patch-src_Bootstrap.h
Comment 3 Jason W. Bacon freebsd_committer freebsd_triage 2020-04-02 00:34:34 UTC 
This would seem to qualify for a blanket MFH approval on the condition that the port is broken in the latest branch.

https://www.freebsd.org/doc/en_US.ISO8859-1/articles/committers-guide/ports.html#ports-qa-quarterly

However, the guide does not indicate how to log this case.

What should go under "Approved by:" in cases like this?
Comment 4 Piotr Kubaj freebsd_committer freebsd_triage 2020-04-02 08:42:44 UTC 
(In reply to Jason W. Bacon from comment #3)
I usually just do:
Approved by: portmgr (fix build blanket)
Comment 5 Jason W. Bacon freebsd_committer freebsd_triage 2020-04-02 13:41:52 UTC 
Fixed, thanks for the patch!
Comment 6 commit-hook freebsd_committer freebsd_triage 2020-04-02 13:42:19 UTC 
A commit references this bug:

Author: jwb
Date: Thu Apr  2 13:41:03 UTC 2020
New revision: 530371
URL: https://svnweb.freebsd.org/changeset/ports/530371

Log:
  MFH: r530250

  kallisto: Patch for build with GCC

  Fixes broken build on GCC-based platforms

  PR:             ports/245240
  Submitted by:   pkubaj

  Approved by:	portmgr (fix build blanket)

Changes:
_U  branches/2020Q2/
  branches/2020Q2/biology/kallisto/Makefile
  branches/2020Q2/biology/kallisto/files/patch-src_Bootstrap.h