#1 Patch to build kmer r1902 on Solaris 11 Express

open
nobody
None
5
2012-12-13
2011-05-25
No

The following patches against kmer (r1902) should sufficiently
enhance portability to allow building on Solaris 11 Express
(I did not test on Solaris 10 due to the default gmake
3.80, which is apparently not supported).

Brief summary:

configure.sh
* Add 64-bit compiler flags & auto-detection for Solaris

atac-driver/chainer/halign/halign.C
libsim4/sim4core/align.C
libutil/sweatShop.C
snapper/thr-search.C
tapper/tapperGlobalData.H
* Solaris defines SS and GS in /usr/include/sys/regset.h;
undef to use as variables

libutil/file.c:
* Include "limits.h" for PATH_MAX (this is specified by POSIX)

libutil/bitPackedArray.C
libkmer/positionDB.C
meryl/build.C
* Use POSIX memset() instead of bzero()

Discussion

  • Nathan Weeks

    Nathan Weeks - 2011-11-08
     
  • Nathan Weeks

    Nathan Weeks - 2011-11-08
     
  • Nathan Weeks

    Nathan Weeks - 2011-11-08
     
  • Nathan Weeks

    Nathan Weeks - 2011-11-08
     
  • Nathan Weeks

    Nathan Weeks - 2011-11-08

    I've attached the patches individually to perhaps make them easier to apply.
    They should not affect compilation on other platforms.
    A minor change: instead of switching bzero() to memset(), these patches simplyinclude "strings.h" for bzero().

    Also, note that my original mod to libutil/file.c suggested a switch from
    statfs() to statvfs(), but I failed to note that the f_bsize member of thestatfs struct is equivalent to the f_frsize member of the statvfs struct.
    statvfs() is POSIX, and is portable between Linux, AIX, and other POSIX OSs.

     

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