Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add missing...

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 679413e0ad15caeac0eb93b5f818030f73262391..090de49e4e0c9e58f82b567a08aab4cefceafefa 100644 (file)
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.73 2015/03/28 18:03:23 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.74 2015/05/07 10:17:54 jlec Exp $
+
+  07 May 2015; Justin Lecher <jlec@gentoo.org> emboss-6.6.0.ebuild,
+  files/emboss-6.6.0_fix-build-system.patch:
+  Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add
+  missing dep, bug #544516
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0-r1.ebuild,
   -emboss-6.3.1_p4.ebuild:

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index 7b459a97d3994f85abd4609c35be8232be350a05..35bc13d1cbd77bbfa2b7b38bee27ca3ab6afc053 100644 (file)
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -8,7 +8,7 @@ AUX README.gentoo 1522 SHA256 3cbb20ef948613f07698ab17c2b432e3aeab0ade6499a965c5
 AUX emboss-5.0.0-as-needed.patch 1751 SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3 SHA512 a2d978ce86fc3a63dc691059c4da598ccfb958d51097bc6070204ad6062f257b3ac496b852bb2772041bda087d0732cf03c4a4868462781700705da4faff8b59 WHIRLPOOL 101b8c89052dbc24211363e4fbe45e1407a30f8046013269d360b983a677ad5e62be796baf1d1097ae30dc392dc8db789d784dad51384e9c9b8df526b475a1d6
 AUX emboss-6.3.1_p4-r1_plcol.patch 3638 SHA256 dfaf85cf5c53a42047a75b1544ca44b450f2d4219c458c243bab53166f917b64 SHA512 63feed3dc32769b1c77ee79c4fd2f7d84d3d9bc6b716bc5f8dbef9ecff441432e7c1030b4d42e2da647231a27b6a7ae094b2115730ba8de94a363644d33ee489 WHIRLPOOL 7ba010b3a3a7eb116e4b0b85734648112fd4a6d780d32bde67a459fe23385b5f73a70d69b67b6d775992227ea90fb5edba21db1e4b51624aabfe5831b590e40d
 AUX emboss-6.6.0_FORTIFY_SOURCE-fix.patch 417 SHA256 317bff2c29f321afe7274babba8db554420a26744cef6aa73885b18e7434e89f SHA512 9873504675825613c913fbd8c03d919c5d70ad7f15e3983ae9dc5ecd04e57d1086c303a4f38efd29def4f089099b24449014bbe965816c7f8b37a5d4ffa13469 WHIRLPOOL b23ea76326c732d5c25429589bed6301d0a6e9342523275a40c225c2af0e25eb2b6279905c52633b35eb3208bf43b7f4a1307c5f66bf95e81e8c8097d967d801
-AUX emboss-6.6.0_fix-build-system.patch 10976 SHA256 5ce7f95c2deaf6ce4f7ffa617f61de6c77dc05b74e420fa57e0562142215b180 SHA512 d03cc98b0dcbf997ab562007e2190c03e8dbbda4ee3d679001bbcdfb0d33afd717560e445f9a463b7b1e36bba59b4accb7318c2a38ffb2fb6283dd3482dbfbfc WHIRLPOOL cc58a4041730d48ce958c0babef2d0185df9bf1738daff88a5b62724ceca27438ea7c8370fafc309d816bf76b80b3c23d063d915dbe59e081ab794da29b38079
+AUX emboss-6.6.0_fix-build-system.patch 12599 SHA256 9ff77b03a1b1d5d28ae7720a6e61ddf226337d04aaf4da69e3c9a5918dcea7de SHA512 60dbb50967b0b855fabd68f2df7713da81007cb84aeb3f2d7510d13e533e3b19ed3d07e012010ebb1b2af04522f6f2142fbef405b9b580740a6bb5d30319b67b WHIRLPOOL 938e9208888fcb180177585c777465b1b2e82588a4a06588b79e85b76f53509c0ce04db6e03258bcb3ccc131c6d815a07b8933474bf98a2ecbe1359595b9892e
 AUX emboss-6.6.0_plplot-declarations.patch 1562 SHA256 d0146d519f23c0bee9c2b13cde1c8f6b4e2ae333740672623620d5236e58326d SHA512 fc27b7c1d518b5cdacf1964d56219c6574f43d18dc324e41b9dcdfd1afef17a784f2b209b62c366fb902ba57a50f438a1b328eb2118ee9463ce82b36039bc0bb WHIRLPOOL d23b7a061d1fa41c8319fd9f00168153022a70575148b6c23cd41d9fa9cf393caddb3d26a4ebcf94b66892998bd356b2ea391f448306706e364603bdbe809153
 AUX emboss-6.6.0_qa-implicit-declarations.patch 1324 SHA256 87de58d0a6225ba7f4644edd802d8c8658d59bd8140b48771da86b849e725b96 SHA512 15c303fe48a438f50f1c9a0efd7e8fcbcb4102151fc182feb8e0d74c47c3435385a1e44436cebd3c2017c97dd89b82832258748f28f3740e511a92b088f539fb WHIRLPOOL d1aeee505672c1ec596afc547052324144f4b72f397722d9e387d94c1940b30f81b8f265d9cd1ef902dea083f628ae79a3a3e5f65bb2342eb54c57fa169ca60a
 AUX emboss-README.Gentoo-1 1474 SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd SHA512 92d6f567d10b6dc9188a736f502b8ab3961d6930424ed8ff3a6d21f9a8037cb94d5d20c9dce186fecd4da4b8cbc2cd842998e4d48a452abf69fc960d9bc9fd7f WHIRLPOOL 0ecc950f391c23afcdf3607ab6ef27a87b7a9b62e5ce15b3bca78166529c9dce7794cfdb181e99993326ee5b512707abfef230425a187b23b0bb8db2adb97af3
@@ -19,25 +19,25 @@ DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e4
 DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c
 EBUILD emboss-6.0.1.ebuild 3462 SHA256 e0b2cc3fa1d46fce803a3054e5a7a37f3e8f532822fe5c4e27c5f13988f3bdfd SHA512 60f0b43ab3377791dd44553a4bbd9817fa498afa7ac1a11c334f20ae3d431aef4e35b9a1b38a572bd185ecb5cd29e69de24f13c90c36b689299bc5b2d2194932 WHIRLPOOL 2fe9a606dc570e8236898fbde67dac4b05ba19eb6c65bbfd13fefb11e6bc2e0fab19c39555cccbcdab734636b9f058f88529816e0878a3db8e40548610cceb0d
 EBUILD emboss-6.3.1_p4-r1.ebuild 3552 SHA256 b98299dbbd7c6fe64de451eccb224935cbd36566b837ec98d672c5e0ecda5571 SHA512 f0d2eafdf5364a4a64011b1ede64e78014a41357187cd746979f12afd30de4135e43a525f856b8f43153fd85863ed306236edfb2848f849a471a8028c298668f WHIRLPOOL 7952605042b63201d5e0aececb9554c06ca8270f1abcbd6e221d59b19803e8fcc38889df0464deed16d874da4970cfb9ad505613092286d0cf2fd1f53b5933e2
-EBUILD emboss-6.6.0.ebuild 1779 SHA256 7590f591ce76ae91a14314ff7fe906a5a7af80348516ada361d19a0e4be93e37 SHA512 2f990414a1e1c1468ca43aa70a9dd5a8c10762a5f299b8c8a292be4d855a2d296780794ad954e6fb433bf931ab243f3e1f9bfe47a51fc6b0354665a4af179ea2 WHIRLPOOL 1b10864dc65760a4e90e2aa71f2d340421fdc7c21ec235c4c1e6efcf406a789fd991906b8383588df786428b69342e6661631df2fbe802b7ffb3b3580d6f068b
-MISC ChangeLog 12843 SHA256 8e35bdad67bcdb0aeaa302d4ada9175f61859f807a44cc1af24c77f98a1500e0 SHA512 ce364bcb88f1ed687fe6058c9815a67ba1f6a56469f6a8d49f13fcbcd8e22ea6e21781aea580a29cb58dfe37c524e972645594ec7fa91bf98d4338ae19e36541 WHIRLPOOL 58db864fdf6fec089205ee1a4f3947d3eda943653813c86f171fceec7aa8dc56b5afbe510f6311be4ddd265fb74aac59469996f829c740f63aa8ea98b65c0164
+EBUILD emboss-6.6.0.ebuild 1841 SHA256 f2156acd471e71d485aad420674263d2cebf043f7a4d14456e3ed4ea96e479cc SHA512 a4a8a753a51c0002629e5fe6e6a529c03d7cabd073377a02b305fcaea23089802d533cc5d342d0f2a802ffd69df7c7c6913b9bcb5e44939fef6c3028b3945ef1 WHIRLPOOL 67ad36185b1f2d877ea56590286b31c3380047d86dcb94674bd068b4cd3ecdebd357ba9d45fb2d2fbee4e8c77b6554722ebc0b88b6d955a43dad86a13e9050b3
+MISC ChangeLog 13064 SHA256 bbadcd01a8da6cec4c556d1d2ad326c80db8edb8c18061cdb40df3a4e50c64b8 SHA512 4a426b8fcea5a36cee40445c8470a516ec91e23bea5cc203bd9d3a169ffade7b574c70c1f0c21cc3755c8c19a0ad06deff0ce403b5cdaa17c4d27b54258a24de WHIRLPOOL d9f7215a2edab57f5960e2de85d23ed44ebb72bfae97457c9b0069ac33123b4696e677e93661bfab3c8d339d58ed67babc2dd524440d9b6c48d7db4132f47737
 MISC metadata.xml 926 SHA256 71766485eac6593e84b57885a4ecdd945700276f699ae0e2f041ef0fa2e4287e SHA512 2da828f1c2eca2eff95c972eadbf48a59a610966a0eac30d45302ff8ff133069121fd8d14e2a1135d866b2a4610b772f6a74445fa1324959dac08ec353284a41 WHIRLPOOL 61c4316c57e6fc9451ef928fa81a0becf2f3c4b3c4fcb2fb23896655b8bd0c1471797d84fa0c86a5502e1c02421f9605b62bbb83ee1893a3d2f7af8167436dfc
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+Version: GnuPG v2.1
 
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diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
index 5343130d128e72b863898316ac33d6dba8b01f81..cca6135771936af0099c90c687e59bbc0e41b8b0 100644 (file)
--- a/sci-biology/emboss/emboss-6.6.0.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild,v 1.1 2015/03/28 17:03:16 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild,v 1.2 2015/05/07 10:17:54 jlec Exp $
 
 EAPI=5
 
@@ -12,12 +12,14 @@ SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
 
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE+=" minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
 
 RDEPEND+=" !sys-devel/cons"
 PDEPEND+="
        !minimal? (
                sci-biology/aaindex
                sci-biology/cutg
+               sci-biology/primer3
                sci-biology/prints
                sci-biology/prosite
                sci-biology/rebase

diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
index c831c3ba7e2878d265d545e7f670b88cfbcbf38e..266bddd95a374c1e0e422bac130f8b3d99617160 100644 (file)
--- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
+++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
@@ -1,5 +1,60 @@
---- EMBOSS-6.6.0/ajax/acd/Makefile.am
-+++ EMBOSS-6.6.0/ajax/acd/Makefile.am
+ Makefile.am               |  9 +++---
+ ajax/Makefile.am          |  4 +--
+ ajax/acd/Makefile.am      |  8 +++--
+ ajax/ajaxdb/Makefile.am   |  6 ++--
+ ajax/core/Makefile.am     |  6 ++--
+ ajax/core/ajreg.h         |  7 ++--
+ ajax/ensembl/Makefile.am  |  6 ++--
+ ajax/graphics/Makefile.am |  8 +++--
+ configure.ac              | 82 ++++++++++++++++++++++++++---------------------
+ emboss/Makefile.am        | 13 +++++---
+ jemboss/lib/Makefile.am   |  2 +-
+ m4/idxdbs.m4              | 17 +++-------
+ nucleus/Makefile.am       |  8 +++--
+ 13 files changed, 100 insertions(+), 76 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 177dec5..18dd99a 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -12,8 +12,11 @@ LICENSE \
+ ONEWS \
+ PROBLEMS
+ 
+-SUBDIRS = \
+-plplot \
++SUBDIRS =
++if !ESYSTEMLIBS
++SUBDIRS += plplot
++endif
++SUBDIRS += \
+ ajax \
+ nucleus \
+ emboss \
+@@ -33,5 +36,3 @@ dist-hook:
+       tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
+       tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
+ 
+-install-exec-hook:
+-      $(bindir)/embossupdate
+diff --git a/ajax/Makefile.am b/ajax/Makefile.am
+index f27472c..de34e17 100644
+--- a/ajax/Makefile.am
++++ b/ajax/Makefile.am
+@@ -1,7 +1,7 @@
+ ## Process this file with automake to produce Makefile.in
+ 
+-SUBDIRS  = pcre
++SUBDIRS  =
+ if !ESYSTEMLIBS
+-SUBDIRS += expat zlib
++SUBDIRS += pcre expat zlib
+ endif
+ SUBDIRS += core graphics ensembl ajaxdb acd
+diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
+index 9f0f700..3295a1d 100644
+--- a/ajax/acd/Makefile.am
++++ b/ajax/acd/Makefile.am
 @@ -3,16 +3,20 @@
  lib_LTLIBRARIES = libacd.la
  
@@ -23,8 +78,10 @@
  libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
  
  libacd_la_LDFLAGS  = -version-info 6:5:0
---- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
-+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
+diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
+index c2b0c00..9de14fe 100644
+--- a/ajax/ajaxdb/Makefile.am
++++ b/ajax/ajaxdb/Makefile.am
 @@ -3,14 +3,16 @@
  lib_LTLIBRARIES = libajaxdb.la
  
@@ -44,8 +101,32 @@
  libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
  libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
  
---- EMBOSS-6.6.0/ajax/core/ajreg.h
-+++ EMBOSS-6.6.0/ajax/core/ajreg.h
+diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
+index 2906837..3189c34 100644
+--- a/ajax/core/Makefile.am
++++ b/ajax/core/Makefile.am
+@@ -3,13 +3,15 @@
+ lib_LTLIBRARIES = libajax.la
+ 
+ libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
+ 
+-libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
++libajax_la_CPPFLAGS  =
+ if !ESYSTEMLIBS
++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+-endif
+ libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
+ libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
+ libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
+diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
+index 1623c82..5d928cf 100644
+--- a/ajax/core/ajreg.h
++++ b/ajax/core/ajreg.h
 @@ -39,9 +39,8 @@
  #include "ajdefine.h"
  #include "ajstr.h"
@@ -58,7 +139,7 @@
  
  AJ_BEGIN_DECLS
  
-@@ -84,7 +83,7 @@
+@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
  
  typedef struct AjSRegexp
  {
@@ -67,28 +148,10 @@
      pcre_extra *extra;
      int *ovector;
      const char* orig;
---- EMBOSS-6.6.0/ajax/core/Makefile.am
-+++ EMBOSS-6.6.0/ajax/core/Makefile.am
-@@ -3,13 +3,15 @@
- lib_LTLIBRARIES = libajax.la
- 
- libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
-+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
- 
--libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
-+libajax_la_CPPFLAGS  =
- if !ESYSTEMLIBS
-+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
--endif
- libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
-+endif
- libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
- libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
- libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
---- EMBOSS-6.6.0/ajax/ensembl/Makefile.am
-+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am
+diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
+index 0d1250b..5484c02 100644
+--- a/ajax/ensembl/Makefile.am
++++ b/ajax/ensembl/Makefile.am
 @@ -3,13 +3,15 @@
  lib_LTLIBRARIES = libensembl.la
  
@@ -107,8 +170,10 @@
  libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
  
  libensembl_la_LDFLAGS  = -version-info 6:5:0
---- EMBOSS-6.6.0/ajax/graphics/Makefile.am
-+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am
+diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
+index a4f202b..1114c2c 100644
+--- a/ajax/graphics/Makefile.am
++++ b/ajax/graphics/Makefile.am
 @@ -3,12 +3,16 @@
  lib_LTLIBRARIES = libajaxg.la
  
@@ -128,21 +193,11 @@
  libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
  
  libajaxg_la_LDFLAGS  = -version-info 6:5:0
---- EMBOSS-6.6.0/ajax/Makefile.am
-+++ EMBOSS-6.6.0/ajax/Makefile.am
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
--SUBDIRS  = pcre
-+SUBDIRS  =
- if !ESYSTEMLIBS
--SUBDIRS += expat zlib
-+SUBDIRS += pcre expat zlib
- endif
- SUBDIRS += core graphics ensembl ajaxdb acd
---- EMBOSS-6.6.0/configure.ac
-+++ EMBOSS-6.6.0/configure.ac
-@@ -629,32 +629,6 @@
+diff --git a/configure.ac b/configure.ac
+index a7bd9c6..9ba3121 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -629,32 +629,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -175,7 +230,7 @@
  dnl Define where the EMBOSS package is located
  AC_SUBST([AJAX_FIXED_ROOT])
  AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
-@@ -743,17 +717,7 @@
+@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -193,24 +248,25 @@
  
  
  
-@@ -849,7 +813,51 @@
+@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs],
  
  AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
  
--
 +AS_IF([test "x${enable_systemlibs}" = "xyes"],
 +[
 +dnl using system libraries
 +  PKG_CHECK_MODULES([PCRE], [libpcre])
 +  PKG_CHECK_MODULES([EXPAT], [expat])
 +  PKG_CHECK_MODULES([ZLIB], [zlib])
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++    [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++    )
 +],
 +[
 +dnl using bundled libraries
 +  dnl PCRE library definitions - see the MAJOR and MINOR values
 +  dnl to see which version's configure.ac these lines come from
-+
+ 
 +  dnl Provide the current PCRE version information. Do not use numbers
 +  dnl with leading zeros for the minor version, as they end up in a C
 +  dnl macro, and may be treated as octal constants. Stick to single
@@ -246,30 +302,33 @@
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- EMBOSS-6.6.0/emboss/Makefile.am
-+++ EMBOSS-6.6.0/emboss/Makefile.am
-@@ -28,15 +28,18 @@
+diff --git a/emboss/Makefile.am b/emboss/Makefile.am
+index 89ada78..f987d40 100644
+--- a/emboss/Makefile.am
++++ b/emboss/Makefile.am
+@@ -28,15 +28,18 @@ endif
  
  AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
  AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
 +AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
  AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
  AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
--AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
- if !ESYSTEMLIBS
-+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
++if !ESYSTEMLIBS
+ AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+-if !ESYSTEMLIBS
  AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
  AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-+AM_CPPFLAGS += -I$(top_srcdir)/plplot
+-endif
+-AM_CPPFLAGS += -I$(top_srcdir)/nucleus
+ AM_CPPFLAGS += -I$(top_srcdir)/plplot
 +else
 +AM_CFLAGS   += $(PLPLOT_CFLAGS)
- endif
- AM_CPPFLAGS += -I$(top_srcdir)/nucleus
--AM_CPPFLAGS += -I$(top_srcdir)/plplot
++endif
++AM_CPPFLAGS += -I$(top_srcdir)/nucleus
  AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
  AM_CPPFLAGS += $(JAVA_CPPFLAGS)
  
-@@ -49,9 +52,11 @@
+@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
  if !ESYSTEMLIBS
  LDADD += ../ajax/zlib/libezlib.la
  LDADD += ../ajax/expat/libeexpat.la
@@ -282,9 +341,11 @@
  LDADD += $(XLIB)
  
  #if PURIFY
---- EMBOSS-6.6.0/jemboss/lib/Makefile.am
-+++ EMBOSS-6.6.0/jemboss/lib/Makefile.am
-@@ -12,7 +12,7 @@
+diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
+index 5f7e21e..8b45ce2 100644
+--- a/jemboss/lib/Makefile.am
++++ b/jemboss/lib/Makefile.am
+@@ -12,7 +12,7 @@ mail.jar \
  jalviewApplet.jar \
  jemboss.jar
  
@@ -293,8 +354,10 @@
  if JAVA_BUILD
        $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
  endif
---- EMBOSS-6.6.0/m4/idxdbs.m4
-+++ EMBOSS-6.6.0/m4/idxdbs.m4
+diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
+index 0ca7ea9..9b54f2a 100644
+--- a/m4/idxdbs.m4
++++ b/m4/idxdbs.m4
 @@ -1,17 +1,8 @@
  AC_DEFUN([CHECK_IDXDBS],
  [
@@ -317,30 +380,10 @@
 +      [],
 +      [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
  ])
---- EMBOSS-6.6.0/Makefile.am
-+++ EMBOSS-6.6.0/Makefile.am
-@@ -12,8 +12,11 @@
- ONEWS \
- PROBLEMS
- 
--SUBDIRS = \
--plplot \
-+SUBDIRS =
-+if !ESYSTEMLIBS
-+SUBDIRS += plplot
-+endif
-+SUBDIRS += \
- ajax \
- nucleus \
- emboss \
-@@ -33,5 +36,3 @@
-       tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
-       tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
- 
--install-exec-hook:
--      $(bindir)/embossupdate
---- EMBOSS-6.6.0/nucleus/Makefile.am
-+++ EMBOSS-6.6.0/nucleus/Makefile.am
+diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
+index 37b8543..5819c89 100644
+--- a/nucleus/Makefile.am
++++ b/nucleus/Makefile.am
 @@ -3,6 +3,7 @@
  lib_LTLIBRARIES = libnucleus.la
  
@@ -349,7 +392,7 @@
  
  if ISSHARED
  if ISAIXIA64
-@@ -10,11 +11,14 @@
+@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
  endif
  endif