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10570c91c8
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)
116 lines
3.4 KiB
C
116 lines
3.4 KiB
C
--- nucleus/embindex.c.orig Mon Jan 23 12:24:54 2006
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+++ nucleus/embindex.c Thu Dec 22 13:12:38 2005
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@@ -973,15 +973,14 @@
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if(!do_ref)
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{
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ajListPop(entry->files,(void **)&tmpstr);
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- ajFmtPrintF(entfile,"%S%S\n",entry->directory,tmpstr);
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+ ajFmtPrintF(entfile,"%S\n",tmpstr);
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ajListPushApp(entry->files,(void *)tmpstr);
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}
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else
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{
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ajListPop(entry->files,(void **)&tmpstr);
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ajListPop(entry->reffiles,(void **)&refstr);
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- ajFmtPrintF(entfile,"%S%S %S%S\n",entry->directory,tmpstr,
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- entry->directory,refstr);
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+ ajFmtPrintF(entfile,"%S %S\n",tmpstr, refstr);
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ajListPushApp(entry->files,(void *)tmpstr);
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ajListPushApp(entry->reffiles,(void *)refstr);
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}
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@@ -1150,7 +1149,15 @@
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entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
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entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
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+ entry->idsecorder = (entry->pagesize - 60) / 24;
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+ entry->idsecfill = (entry->pagesize - 60) / 20;
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+ entry->acsecorder = (entry->pagesize - 60) / 24;
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+ entry->acsecfill = (entry->pagesize - 60) / 20;
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+
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+ entry->svsecorder = (entry->pagesize - 60) / 24;
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+ entry->svsecfill = (entry->pagesize - 60) / 20;
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+
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ajStrDel(&value);
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return;
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@@ -1183,28 +1190,38 @@
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if(entry->do_id)
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{
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- entry->idcache = ajBtreeCacheNewC(basenam,ID_EXTENSION,idir,"w+",
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- entry->pagesize, entry->idorder,
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- entry->idfill, level,
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- entry->cachesize);
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+ entry->idcache = ajBtreeSecCacheNewC(basenam,ID_EXTENSION,idir,"w+",
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+ entry->pagesize, entry->idorder,
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+ entry->idfill, level,
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+ entry->cachesize,
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+ entry->idsecorder, slevel,
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+ entry->idsecfill, count,
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+ entry->kwlen);
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ajBtreeCreateRootNode(entry->idcache,0L);
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}
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if(entry->do_accession)
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{
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- entry->accache = ajBtreeCacheNewC(basenam,AC_EXTENSION,idir,"w+",
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- entry->pagesize, entry->acorder,
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- entry->acfill, level,
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- entry->cachesize);
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+ entry->accache = ajBtreeSecCacheNewC(basenam,AC_EXTENSION,idir,"w+",
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+ entry->pagesize,
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+ entry->acorder, entry->acfill,
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+ level,
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+ entry->cachesize,
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+ entry->acsecorder, slevel,
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+ entry->acsecfill, count,
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+ entry->kwlen);
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ajBtreeCreateRootNode(entry->accache,0L);
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}
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if(entry->do_sv)
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{
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- entry->svcache = ajBtreeCacheNewC(basenam,SV_EXTENSION,idir,"w+",
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- entry->pagesize, entry->svorder,
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- entry->svfill, level,
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- entry->cachesize);
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+ entry->svcache = ajBtreeSecCacheNewC(basenam,SV_EXTENSION,idir,"w+",
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+ entry->pagesize, entry->svorder,
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+ entry->svfill, level,
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+ entry->cachesize,
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+ entry->svsecorder, slevel,
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+ entry->svsecfill, count,
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+ entry->kwlen);
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ajBtreeCreateRootNode(entry->svcache,0L);
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}
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@@ -1270,18 +1287,27 @@
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if(entry->do_id)
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{
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+ ajBtreeFreePriArray(entry->idcache);
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+ ajBtreeFreeSecArray(entry->idcache);
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+
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ajBtreeCacheSync(entry->idcache,0L);
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ajBtreeCacheDel(&entry->idcache);
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}
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if(entry->do_accession)
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{
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+ ajBtreeFreePriArray(entry->accache);
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+ ajBtreeFreeSecArray(entry->accache);
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+
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ajBtreeCacheSync(entry->accache,0L);
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ajBtreeCacheDel(&entry->accache);
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}
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if(entry->do_sv)
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{
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+ ajBtreeFreePriArray(entry->svcache);
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+ ajBtreeFreeSecArray(entry->svcache);
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+
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ajBtreeCacheSync(entry->svcache,0L);
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ajBtreeCacheDel(&entry->svcache);
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}
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