[Bug 232929] biology/bowtie fails to build with GCC 8

[bugzilla-noreply at freebsd.org]

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=232929

            Bug ID: 232929
           Summary: biology/bowtie fails to build with GCC 8
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: Individual Port(s)
          Assignee: jwb at freebsd.org
          Reporter: gerald at FreeBSD.org
            Blocks: 231590
             Flags: maintainer-feedback?(jwb at freebsd.org)
          Assignee: jwb at freebsd.org

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 ?


Referenced Bugs:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=231590
[Bug 231590] [exp-run] Update GCC_DEFAULT from 7 to 8
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