[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. debian/6.3.1-3-6-g77d8c7c
Charles Plessy
plessy at debian.org
Thu Aug 12 01:13:42 UTC 2010
The following commit has been merged in the master branch:
commit 2436f81ee46195fd5cf13d0060349b020b4b8022
Author: Charles Plessy <plessy at debian.org>
Date: Thu Aug 12 08:00:02 2010 +0900
# New upstream patch.
URL: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz
diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
index fd8e550..56c7a5c 100644
--- a/debian/patches/official-upstream-patch.patch
+++ b/debian/patches/official-upstream-patch.patch
@@ -18,11 +18,847 @@ Description: Official upstream patch.
mysql.m4 file - it is unnecessary for the operation of the
EMBOSS distribution. Using this patch will not cause the
libtool problem described above.
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
+ .
+ .
+ Fix 3. EMBOSS-6.3.1/ajax/graphics/ajgraph.c
+ .
+ 9 Aug 2010: Fix potential crash using -debug
+ .
+ .
+ Fix 4. EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
+ EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
+ .
+ 9 Aug 2010: Allow two Ensembl sequences to be loaded without re-registering.
+ Fix Ensembl Genomes registration.
+ Fix Ensembl Genomes identifiers for species without stable
+ identifiers. If the identifier does not obey a stable identifier
+ pattern, it is matched against Exons, Transcripts and
+ Translations in exactly that order.
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz
Forwarded: not-needed
+diff -c -N --recursive -a EMBOSS-6.3.1old/ajax/ajaxdb/ajseqdb.c EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c
+*** EMBOSS-6.3.1old/ajax/ajaxdb/ajseqdb.c 2010-07-06 15:15:52.000000000 +0100
+--- EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c 2010-08-09 17:17:27.000000000 +0100
+***************
+*** 8265,8271 ****
+
+ /* "^%S([EGTP])[0-9]{11,11}" */
+
+! expression = ajFmtStr("^%S([EGTP])", prefix);
+
+ break;
+
+--- 8265,8272 ----
+
+ /* "^%S([EGTP])[0-9]{11,11}" */
+
+! if(prefix)
+! expression = ajFmtStr("^%S([EGTP])", prefix);
+
+ break;
+
+***************
+*** 8275,8281 ****
+
+ /* "^OTT...([EGTP])[0-9]{11,11}" */
+
+! expression = ajStrNewC("^OTT...([EGTP])");
+
+ break;
+
+--- 8276,8283 ----
+
+ /* "^OTT...([EGTP])[0-9]{11,11}" */
+
+! if(prefix)
+! expression = ajStrNewC("^OTT...([EGTP])");
+
+ break;
+
+***************
+*** 8285,8291 ****
+
+ /* "^%SEST([EGTP])[0-9]{11,11}" */
+
+! expression = ajFmtStr("^%SEST([EGTP])", prefix);
+
+ break;
+
+--- 8287,8294 ----
+
+ /* "^%SEST([EGTP])[0-9]{11,11}" */
+
+! if(prefix)
+! expression = ajFmtStr("^%SEST([EGTP])", prefix);
+
+ break;
+
+***************
+*** 8339,8345 ****
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! ajStrNewS(se->Identifier));
+
+ break;
+
+--- 8342,8348 ----
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! (void *) ajStrNewS(se->Identifier));
+
+ break;
+
+***************
+*** 8405,8411 ****
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! ajStrNewS(se->Identifier));
+
+ break;
+
+--- 8408,8414 ----
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! (void *) ajStrNewS(se->Identifier));
+
+ break;
+
+***************
+*** 8465,8471 ****
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! ajStrNewS(se->Identifier));
+
+ break;
+
+--- 8468,8474 ----
+ "'entry'.\n");
+
+ ajListPushAppend(se->StableIdentifiers,
+! (void *) ajStrNewS(se->Identifier));
+
+ break;
+
+***************
+*** 8511,8516 ****
+--- 8514,8596 ----
+ }
+ }
+
++ if(!ajStrGetLen(se->ObjectType))
++ {
++ /*
++ ** An Ensembl Object type could not be established.
++ ** For AJAX Sequence Queries of type ENTRY it is possible to
++ ** test whether this is a stable identifier of any Ensembl
++ ** *Core* Object type.
++ */
++
++ if(qry->Type == QRY_ENTRY)
++ {
++ /* Only use the Ensembl Database Adaptor of type Core. */
++
++ se->DatabaseAdaptor = ensRegistryGetDatabaseadaptor(
++ ensEDatabaseadaptorGroupCore,
++ se->Species);
++
++ /* Check if this is an Ensembl Exon. */
++
++ ea = ensRegistryGetExonadaptor(se->DatabaseAdaptor);
++
++ ensExonadaptorFetchByStableIdentifier(ea,
++ se->Identifier,
++ 0,
++ &exon);
++
++ if(exon)
++ {
++ ajListPushAppend(se->StableIdentifiers,
++ (void *) ajStrNewS(se->Identifier));
++
++ ajStrAssignC(&se->ObjectType, "E");
++ }
++
++ /* Check if this is an Ensembl Transcript. */
++
++ tca = ensRegistryGetTranscriptadaptor(se->DatabaseAdaptor);
++
++ ensTranscriptadaptorFetchByStableIdentifier(tca,
++ se->Identifier,
++ 0,
++ &transcript);
++
++ if(transcript && (!ajStrGetLen(se->ObjectType)))
++ {
++ ajListPushAppend(se->StableIdentifiers,
++ (void *) ajStrNewS(se->Identifier));
++
++ ajStrAssignC(&se->ObjectType, "T");
++ }
++
++ /* Check if this is an Ensembl Translation. */
++
++ tla = ensRegistryGetTranslationadaptor(se->DatabaseAdaptor);
++
++ ensTranslationadaptorFetchByStableIdentifier(tla,
++ se->Identifier,
++ 0,
++ &translation);
++
++ if(translation && (!ajStrGetLen(se->ObjectType)))
++ {
++ ajListPushAppend(se->StableIdentifiers,
++ (void *) ajStrNewS(se->Identifier));
++
++ ajStrAssignC(&se->ObjectType, "P");
++ }
++ }
++ else
++ ajWarn("Since this species does not seem to have a "
++ "stable identifier schema defined in the 'meta' "
++ "table or the identifier type could not be "
++ "established, only queries for single entries can "
++ "be matched against Exons, Transcripts or "
++ "Transaltions.");
++ }
++
+ /* The query has finished at this stage. */
+
+ qry->TotalEntries = ajListGetLength(se->StableIdentifiers);
+diff -c -N --recursive -a EMBOSS-6.3.1old/ajax/ensembl/ensregistry.c EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
+*** EMBOSS-6.3.1old/ajax/ensembl/ensregistry.c 2010-07-06 15:11:39.000000000 +0100
+--- EMBOSS-6.3.1/ajax/ensembl/ensregistry.c 2010-08-09 17:17:40.000000000 +0100
+***************
+*** 398,403 ****
+--- 398,405 ----
+
+ static AjPList registryIdentifiers = NULL;
+
++ static AjPList registrySources = NULL;
++
+ static RegistryPIdentifier registryIdentifierNew(
+ AjPStr expression,
+ AjPStr species,
+***************
+*** 424,429 ****
+--- 426,434 ----
+
+ static void registryEntryDel(RegistryPEntry *Pentry);
+
++ static AjBool registrySourceCheckAndRegister(const AjPStr source,
++ AjBool *Pregistered);
++
+ static AjPStr registryCheckAlias(const AjPStr alias);
+
+ static AjBool registryLoadAliasesFromDatabaseconnection(
+***************
+*** 1057,1062 ****
+--- 1062,1122 ----
+
+
+
++ /* @funcstatic registrySourceCheckAndRegister *********************************
++ **
++ ** Check if a source has been registered in the AJAX List of Registry source
++ ** before. If this was not the case automatically register it.
++ **
++ ** @param [r] source [const AjPStr] Ensembl Registry source
++ ** @param [w] Pregistered [AjBool*] Registered boolean
++ ** ajTrue if registered before, ajFalse if not
++ **
++ ** @return [AjBool] ajTrue opon success, ajFalse otherwise
++ ** @@
++ ******************************************************************************/
++
++ static AjBool registrySourceCheckAndRegister(const AjPStr source,
++ AjBool *Pregistered)
++ {
++ AjIList iterator = NULL;
++
++ AjPStr entry = NULL;
++
++ if(!Pregistered)
++ return ajFalse;
++
++ *Pregistered = ajFalse;
++
++ if(!(source && ajStrGetLen(source)))
++ return ajFalse;
++
++ iterator = ajListIterNew(registrySources);
++
++ while(!ajListIterDone(iterator))
++ {
++ entry = (AjPStr) ajListIterGet(iterator);
++
++ if(ajStrMatchCaseS(entry, source))
++ {
++ *Pregistered = ajTrue;
++
++ break;
++ }
++ }
++
++ ajListIterDel(&iterator);
++
++ /* If this source has not been seen before, add it to the AJAX List. */
++
++ if(!*Pregistered)
++ ajListPushAppend(registrySources, (void *) ajStrNewS(source));
++
++ return ajTrue;
++ }
++
++
++
++
+ /* @filesection ensregistry ***************************************************
+ **
+ ** @nam1rule ens Function belongs to the AJAX Ensembl library
+***************
+*** 1103,1108 ****
+--- 1163,1170 ----
+
+ registryIdentifiers = ajListNew();
+
++ registrySources = ajListstrNew();
++
+ return;
+ }
+
+***************
+*** 1123,1129 ****
+ void **valarray = NULL;
+
+ register ajuint i = 0;
+!
+ if(!registryEntries)
+ return;
+
+--- 1185,1191 ----
+ void **valarray = NULL;
+
+ register ajuint i = 0;
+!
+ if(!registryEntries)
+ return;
+
+***************
+*** 1162,1168 ****
+ /* Free the AJAX Table of aliases. */
+
+ if(registryAliases)
+! ajTablestrFree(®istryAliases);
+
+ /* Clear and free the AJAX Table of Registry Entries. */
+
+--- 1224,1230 ----
+ /* Free the AJAX Table of aliases. */
+
+ if(registryAliases)
+! ajTablestrFree(®istryAliases);
+
+ /* Clear and free the AJAX Table of Registry Entries. */
+
+***************
+*** 1183,1188 ****
+--- 1245,1255 ----
+ ajListFree(®istryIdentifiers);
+ }
+
++ /* Clear and free the AJAX List of Registry Sources. */
++
++ if(registrySources)
++ ajListstrFree(®istrySources);
++
+ return;
+ }
+
+***************
+*** 1768,1774 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 1835,1841 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 1871,1877 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 1938,1944 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 1975,1981 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 2042,2048 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 2339,2345 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 2406,2412 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 2572,2578 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 2639,2645 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 2978,2984 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+--- 3045,3051 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ break;
+
+ default:
+***************
+*** 6281,6287 ****
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ /* Ensembl Database Adaptor groups without a 'meta' table. */
+
+ break;
+--- 6348,6354 ----
+ case ensEDatabaseadaptorGroupWebsite:
+
+ case ensEDatabaseadaptorGroupProduction:
+!
+ /* Ensembl Database Adaptor groups without a 'meta' table. */
+
+ break;
+***************
+*** 6410,6416 ****
+
+ AjBool ensRegistryLoadFromServer(EnsPDatabaseconnection dbc)
+ {
+! AjBool debug = AJFALSE;
+
+ AjPRegexp multire = NULL;
+ AjPRegexp speciesre = NULL;
+--- 6477,6484 ----
+
+ AjBool ensRegistryLoadFromServer(EnsPDatabaseconnection dbc)
+ {
+! AjBool debug = AJFALSE;
+! AjBool registered = AJFALSE;
+
+ AjPRegexp multire = NULL;
+ AjPRegexp speciesre = NULL;
+***************
+*** 6426,6431 ****
+--- 6494,6500 ----
+ AjPStr prefix = NULL;
+ AjPStr swversion = NULL;
+ AjPStr multi = NULL;
++ AjPStr source = NULL;
+
+ EnsEDatabaseadaptorGroup egroup = ensEDatabaseadaptorGroupNULL;
+
+***************
+*** 6440,6460 ****
+ dbc);
+
+ ensDatabaseconnectionTrace(dbc, 1);
+ }
+
+ if(!dbc)
+ return ajFalse;
+
+! multi = ajStrNewC("DEFAULT");
+
+ collectionre =
+! ajRegCompC("^\\w+_collection_([a-z]+)(?:_\\d+)??_(\\d+)_\\w+");
+
+ multire =
+! ajRegCompC("^ensembl_([a-z]+)(?:_\\w+?)*?_(\\d+)");
+
+ speciesre =
+! ajRegCompC("^([a-z]+_[a-z0-9]+)_([a-z]+)(?:_\\d+)??_(\\d+)_\\w+");
+
+ statement = ajStrNewC("SHOW DATABASES");
+
+--- 6509,6554 ----
+ dbc);
+
+ ensDatabaseconnectionTrace(dbc, 1);
++
++ ajDebug("ensRegistryLoadFromServer software version '%s'.\n",
++ registrySoftwareVersion);
+ }
+
+ if(!dbc)
+ return ajFalse;
+
+! /* Check if this Ensembl Database Connection has been used before. */
+!
+! /* NOTE: The following function is in the CVS repository post
+! ** EMBOSS release 6.3.1, but not in the patch.
+! **
+! ** ensDatabaseconnectionFetchUrl(dbc, &source);
+! */
+!
+! source = ajFmtStr("%s://%S@%S:%S/%S",
+! ajSqlconnectionClientToChar(dbc->SqlconnectionClient),
+! dbc->UserName,
+! dbc->HostName,
+! dbc->HostPort,
+! dbc->DatabaseName);
+!
+! registrySourceCheckAndRegister(source, ®istered);
+!
+! ajStrDel(&source);
+!
+! if(registered)
+! return ajTrue;
+!
+! multi = ajStrNewC("default");
+
+ collectionre =
+! ajRegCompC("^\\w+_collection_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
+
+ multire =
+! ajRegCompC("^ensembl_([a-z]+)(_\\w+?)*?(?:_\\d+)?_(\\d+)$");
+
+ speciesre =
+! ajRegCompC("^([a-z]+_[a-z0-9]+)_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
+
+ statement = ajStrNewC("SHOW DATABASES");
+
+***************
+*** 6491,6498 ****
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer matched "
+! "collection database '%S'.\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+--- 6585,6592 ----
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer '%S' "
+! "collection matched\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+***************
+*** 6504,6593 ****
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
+
+ ajStrDel(&group);
+ ajStrDel(&swversion);
+ }
+! else if(ajRegExec(speciesre, dbname))
+ {
+! /* Species-specific databases */
+
+- prefix = ajStrNew();
+ group = ajStrNew();
+ swversion = ajStrNew();
+
+! ajRegSubI(speciesre, 1, &prefix);
+! ajRegSubI(speciesre, 2, &group);
+! ajRegSubI(speciesre, 3, &swversion);
+
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer matched "
+! "species-specific database '%S'.\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+
+ if(egroup)
+! {
+! dba = ensRegistryNewDatabaseadaptor(dbc,
+! dbname,
+! prefix,
+! egroup,
+! ajFalse,
+! 0);
+!
+! registryLoadAliasesFromDatabaseconnection(dbc, dba);
+! }
+ else
+ ajDebug("ensRegistryLoadFromServer got unexpected group "
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
+
+- ajStrDel(&prefix);
+ ajStrDel(&group);
+ ajStrDel(&swversion);
+ }
+! else if(ajRegExec(multire, dbname))
+ {
+! /* Multi-species databases */
+
+ group = ajStrNew();
+ swversion = ajStrNew();
+
+! ajRegSubI(multire, 1, &group);
+! ajRegSubI(multire, 2, &swversion);
+
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer matched "
+! "multi-species database '%S'.\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+
+ if(egroup)
+! ensRegistryNewDatabaseadaptor(dbc,
+! dbname,
+! multi,
+! egroup,
+! ajFalse,
+! 0);
+ else
+ ajDebug("ensRegistryLoadFromServer got unexpected group "
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
+
+ ajStrDel(&group);
+ ajStrDel(&swversion);
+ }
+ else
+! ajDebug("ensRegistryLoadFromServer could not match "
+! "database name '%S'.\n", dbname);
+
+ ajStrDel(&dbname);
+ }
+--- 6598,6725 ----
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
++ else
++ {
++ if(debug)
++ ajDebug("ensRegistryLoadFromServer '%S' "
++ "collection\n",
++ dbname);
++
++ }
+
+ ajStrDel(&group);
+ ajStrDel(&swversion);
+ }
+! else if(ajRegExec(multire, dbname))
+ {
+! /* Multi-species databases */
+
+ group = ajStrNew();
++ prefix = ajStrNew();
+ swversion = ajStrNew();
+
+! ajRegSubI(multire, 1, &group);
+!
+! if(ajRegLenI(multire, 3))
+! {
+! ajRegSubI(multire, 2, &prefix);
+! ajRegSubI(multire, 3, &swversion);
+! }
+! else
+! ajRegSubI(multire, 2, &swversion);
+
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer '%S' "
+! "multi-species matched\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+
+ if(egroup)
+! ensRegistryNewDatabaseadaptor(dbc,
+! dbname,
+! (ajStrGetLen(prefix))
+! ? prefix : multi,
+! egroup,
+! ajFalse,
+! 0);
+ else
+ ajDebug("ensRegistryLoadFromServer got unexpected group "
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
++ else
++ {
++ if(debug)
++ ajDebug("ensRegistryLoadFromServer '%S' "
++ "multi-species\n",
++ dbname);
++ }
+
+ ajStrDel(&group);
++ ajStrDel(&prefix);
+ ajStrDel(&swversion);
+ }
+! else if(ajRegExec(speciesre, dbname))
+ {
+! /* Species-specific databases */
+
++ prefix = ajStrNew();
+ group = ajStrNew();
+ swversion = ajStrNew();
+
+! ajRegSubI(speciesre, 1, &prefix);
+! ajRegSubI(speciesre, 2, &group);
+! ajRegSubI(speciesre, 3, &swversion);
+!
+! /*
+! if(debug)
+! ajDebug("ensRegistryLoadFromServer parsed database '%S' into "
+! "prefix '%S', group '%S' and swversion '%S.\n",
+! dbname, prefix, group, swversion);
+! */
+
+ if(ajStrMatchCaseC(swversion, registrySoftwareVersion))
+ {
+ if(debug)
+! ajDebug("ensRegistryLoadFromServer '%S' "
+! "species-specific matched\n",
+ dbname);
+
+ egroup = ensDatabaseadaptorGroupFromStr(group);
+
+ if(egroup)
+! {
+! dba = ensRegistryNewDatabaseadaptor(dbc,
+! dbname,
+! prefix,
+! egroup,
+! ajFalse,
+! 0);
+!
+! registryLoadAliasesFromDatabaseconnection(dbc, dba);
+! }
+ else
+ ajDebug("ensRegistryLoadFromServer got unexpected group "
+ "string '%S' for database name '%S'.\n",
+ group, dbname);
+ }
++ else
++ {
++ if(debug)
++ ajDebug("ensRegistryLoadFromServer '%S' "
++ "species-specific\n",
++ dbname);
++ }
+
++ ajStrDel(&prefix);
+ ajStrDel(&group);
+ ajStrDel(&swversion);
+ }
+ else
+! ajDebug("ensRegistryLoadFromServer '%S' no match\n", dbname);
+
+ ajStrDel(&dbname);
+ }
+diff -c -N --recursive -a EMBOSS-6.3.1old/ajax/graphics/ajgraph.c EMBOSS-6.3.1/ajax/graphics/ajgraph.c
+*** EMBOSS-6.3.1old/ajax/graphics/ajgraph.c 2010-07-19 12:40:00.000000000 +0100
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2010-08-09 17:17:15.000000000 +0100
+***************
+*** 9843,9849 ****
+
+ plargv[0] = argname;
+ plargv[1] = MAJSTRGETPTR(ajUtilGetProgram());
+! ajDebug("=g= plparseopts('%S', '%s') ajUtilGetProgram\n",
+ plargv[0], plargv[1]);
+
+ plparseopts(&plargc, plargv,
+--- 9843,9849 ----
+
+ plargv[0] = argname;
+ plargv[1] = MAJSTRGETPTR(ajUtilGetProgram());
+! ajDebug("=g= plparseopts('%s', '%s') ajUtilGetProgram\n",
+ plargv[0], plargv[1]);
+
+ plparseopts(&plargc, plargv,
diff -c -N --recursive -a EMBOSS-6.3.1old/configure EMBOSS-6.3.1/configure
*** EMBOSS-6.3.1old/configure 2010-07-19 12:55:36.000000000 +0100
---- EMBOSS-6.3.1/configure 2010-08-06 09:06:53.000000000 +0100
+--- EMBOSS-6.3.1/configure 2010-08-09 17:15:35.000000000 +0100
***************
*** 14481,14488 ****
--
The European Molecular Biology Open Software Suite.
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