cvs commit: ports UPDATING ports/biology/emboss Makefile distinfo pkg-message pkg-plist ports/biology/emboss/files patch-ajindex.c patch-ajindex.h patch-ajpdb.c patch-ajseqdb.c patch-dbxfasta.c patch-dbxflat.c patch-dbxgcg.c patch-embindex.c patch-embindex.h ...

[Thierry Thomas]

thierry     2006-03-31 09:43:22 UTC

  FreeBSD ports repository

  Modified files:
    .                    UPDATING 
    biology/emboss       Makefile distinfo pkg-plist 
    biology/embassy      Makefile distinfo pkg-plist 
  Added files:
    biology/emboss/files patch-ajindex.c patch-ajindex.h 
                         patch-ajpdb.c patch-ajseqdb.c 
                         patch-dbxfasta.c patch-dbxflat.c 
                         patch-dbxgcg.c patch-embindex.c 
                         patch-embindex.h 
                         patch-emboss.default.template 
                         patch-marscan.c pkg-message.in 
                         pre-install.in 
  Removed files:
    biology/emboss       pkg-message 
    biology/embassy/files domainatrix-patch-Makefile.in 
                          emnu-patch-Makefile.in 
  Log:
  For EMBOSS:
  
          This patch brings EMBOSS up to date with the current version.
  
          i.   The patches included in files/ are bugfixes for files in
               EMBOSS-3.0.0 that appeared after the release. They are
               documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README
  
               This is just 'for the record' so that we remember to remove these
               patches in the next update.
  
          ii.  EMBOSS is now installed by default in LOCALBASE/emboss
               This is to avoid CONFLICTS with other ports that install files
               with the same names. Installing EMBOSS to another PREFIX is also
               possible.
  
          iii. now EMBASSY and EMBOSS both store their distfiles in the same
               DIST_SUBDIR
  
          iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
               (manual) way
  
          For EMBASSY:
  
          This update brings embassy in sync with the update of EMBOSS to 3.0.0.
  
          Things that changed from previous version of the port:
  
          i.  embassy now installs by default in $LOCALBASE/emboss (the
              new default PREFIX for emboss as well).
  
          ii. changed DIST_SUBDIR so that all the distfiles are put together with
              emboss. This makes sense(TM)
  
          iii. incorporated new EMBASSY apps (this accounts for the changes in
               OPTIONS and pkg-plist)
  
          iv.  removed obsoleted patches
  
          Finally, I included a sample text that could go in UPDATING.
  
  PR:             93053
  Submitted by:   Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
  
  Revision  Changes      Path
  1.304     +17 -1       ports/UPDATING
  1.6       +22 -18      ports/biology/embassy/Makefile
  1.4       +39 -24      ports/biology/embassy/distinfo
  1.2       +0 -11       ports/biology/embassy/files/domainatrix-patch-Makefile.in (dead)
  1.2       +0 -11       ports/biology/embassy/files/emnu-patch-Makefile.in (dead)
  1.3       +177 -124    ports/biology/embassy/pkg-plist
  1.47      +15 -14      ports/biology/emboss/Makefile
  1.26      +3 -3        ports/biology/emboss/distinfo
  1.1       +5134 -0     ports/biology/emboss/files/patch-ajindex.c (new)
  1.1       +170 -0      ports/biology/emboss/files/patch-ajindex.h (new)
  1.1       +67 -0       ports/biology/emboss/files/patch-ajpdb.c (new)
  1.1       +195 -0      ports/biology/emboss/files/patch-ajseqdb.c (new)
  1.1       +89 -0       ports/biology/emboss/files/patch-dbxfasta.c (new)
  1.1       +146 -0      ports/biology/emboss/files/patch-dbxflat.c (new)
  1.1       +96 -0       ports/biology/emboss/files/patch-dbxgcg.c (new)
  1.1       +115 -0      ports/biology/emboss/files/patch-embindex.c (new)
  1.1       +96 -0       ports/biology/emboss/files/patch-embindex.h (new)
  1.1       +20 -0       ports/biology/emboss/files/patch-emboss.default.template (new)
  1.1       +72 -0       ports/biology/emboss/files/patch-marscan.c (new)
  1.1       +27 -0       ports/biology/emboss/files/pkg-message.in (new)
  1.1       +21 -0       ports/biology/emboss/files/pre-install.in (new)
  1.7       +0 -22       ports/biology/emboss/pkg-message (dead)
  1.23      +1684 -1599  ports/biology/emboss/pkg-plist