Bug 232929

Summary: biology/bowtie fails to build with GCC 8
Product: Ports & Packages Reporter: Gerald Pfeifer <gerald>
Component: Individual Port(s)Assignee: Jason W. Bacon <jwb>
Status: Closed FIXED    
Severity: Affects Some People    
Priority: ---    
Version: Latest   
Hardware: Any   
OS: Any   
Bug Depends on:    
Bug Blocks: 231590    

Description Gerald Pfeifer freebsd_committer freebsd_triage 2018-11-03 12:34:33 UTC 
biology/bowtie has the following bit

  # FIXME: bowtie-align intermittently dumps core when compiled with clang
  # GCC 4.2 does not provide good performance
  USE_GCC=        yes

alas it now fails to build with GCC 8, blocking the update of the default
version of GCC.

Cf. http://package22.nyi.freebsd.org/data/112amd64-default-PR231590/2018-10-29_06h48m05s/logs/errors/bowtie-1.1.2_6.log

ebwt.h: In member function 'uint32_t* Ebwt<TStr>::isa() const':
ebwt.h:863:44: error: cannot convert 'TIndexOffU* const' {aka 'long unsigned int* const'} to 'uint32_t*' {aka 'unsigned int*'} in return
  uint32_t*   isa() const          { return _isa; } /* check */
                                            ^~~~


How about retiring this port in favor of biology/bowtie2 ?
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2018-11-03 21:06:34 UTC 
We generally want to avoid removing scientific ports unless they become very difficult to maintain, since researchers may need to reproduce results years after the initial analysis, e.g. for grant renewals.  There's a simple workaround for this one, which I'll commit shortly,
Comment 2 commit-hook freebsd_committer freebsd_triage 2018-11-03 23:25:08 UTC 
A commit references this bug:

Author: jwb
Date: Sat Nov  3 23:24:30 UTC 2018
New revision: 483954
URL: https://svnweb.freebsd.org/changeset/ports/483954

Log:
  biology/bowtie: Patch for gcc8 and clean up

  PR:             232929
  Reported by:    gerald
  Approved by:    jrm (mentor, implicit)

Changes:
  head/biology/bowtie/Makefile
  head/biology/bowtie/files/patch-ebwt.h
Comment 3 Gerald Pfeifer freebsd_committer freebsd_triage 2018-11-04 11:06:29 UTC 
(In reply to Jason W. Bacon from comment #1)
> We generally want to avoid removing scientific ports unless they become
> very difficult to maintain, since researchers may need to reproduce results
> years after the initial analysis, e.g. for grant renewals.  There's a simple
> workaround for this one, which I'll commit shortly,

Thank you, Jason! That was quick. :-) 

And the explanation on keeping the original version of bowtie in
addition to bowtie2 does make sense.

(You haven't closed the PR yet, so I'll just move it to "In Progress"
based on your commit.)
Comment 4 Jason W. Bacon freebsd_committer freebsd_triage 2018-11-04 14:23:08 UTC 
Tested with USE_GCC=8.  Should be OK now.