Update buildsystem for latest plplot, bug #552492

Package-Manager: portage-2.2.20/cvs/Linux x86_64 Manifest-Sign-Key: 0xE9402A79B03529A2!
author: Justin Lecher <jlec@gentoo.org> 2015-06-21 09:18:27 +0000
committer: Justin Lecher <jlec@gentoo.org> 2015-06-21 09:18:27 +0000
commit: 609992e8e730a2f883e43399c2d06406102a08a6 (patch)
tree: eda0114aa3c8bf435aa0f5976a184f77288524f7 /sci-biology
parent: Drop unneeded -ppc. (diff)
download: historical-609992e8e730a2f883e43399c2d06406102a08a6.tar.gz
historical-609992e8e730a2f883e43399c2d06406102a08a6.tar.bz2
historical-609992e8e730a2f883e43399c2d06406102a08a6.zip
30 files changed, 486 insertions, 328 deletions
diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog
index bef564a95604..b3da1f887501 100644
--- a/sci-biology/embassy-esim4/ChangeLog
+++ b/sci-biology/embassy-esim4/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-esim4
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.33 2015/03/28 18:01:21 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.34 2015/06/21 09:01:36 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-esim4-1.0.0.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-esim4-1.0.0-r6.ebuild,
   embassy-esim4-1.0.0.650.ebuild:
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
index 6872b54f4b76..c3197621d835 100644
--- a/sci-biology/embassy-esim4/Manifest
+++ b/sci-biology/embassy-esim4/Manifest
@@ -1,30 +1,30 @@
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 Hash: SHA512
 
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+AUX embassy-esim4-1.0.0.650_fix-build-system.patch 3167 SHA256 25d191cabc62f3651e7f0cd999573b788827a2f3fb75e5c7be7716797c511577 SHA512 c8f4468998b1e91122e4ee5f355c5db451fa889892c05125edcc2f734051410251de85a9d7aaf5566dc802240d2925c709cfd448c8f96351aaa91c124eb1396f WHIRLPOOL 1558f5aca98ef8e6742c5990e7bb604d99ff80d6994147e01e2b1a3afc1c50e5efb56b9649d228da90bd955c83e3e12b65cfdc45c3bd50667de0c4236229be6b
 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
 DIST embassy-6.0.1-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
 DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62
 EBUILD embassy-esim4-1.0.0-r5.ebuild 519 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab SHA512 23b41eea8b3c0dd1f41887305afa18596cc82e6853e83355399a81545932c95c661760df2d926b1fd295bb04554e471f3926669808c0a625813216dc3e3750c3 WHIRLPOOL 47d8e921988c76e15d5a77adafe5df01b655be2a9d60201a139a098b2b45252b81befc23f6e5b8813bf71a64c6c843f676c99f194a7b2cb9b5e5902fd1388771
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diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
index 8279071806c6..ead54c91b5f3 100644
--- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
@@ -1,6 +1,13 @@
---- ESIM4-1.0.0.650/configure.ac
-+++ ESIM4-1.0.0.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 924220a..2c45f46 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +41,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +63,34 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- ESIM4-1.0.0.650/src/Makefile.am
-+++ ESIM4-1.0.0.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 0620938..0304bb8 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,17 +101,10 @@
  endif
  
  if ISSHARED
-@@ -63,5 +61,5 @@
+@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
 -        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
 +        -lajax $(NLADD) $(XLIB)
  endif
---- ESIM4-1.0.0.650/emboss_acd/Makefile.am
-+++ ESIM4-1.0.0.650/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog
index e13c9d1a94ee..174dac9fac61 100644
--- a/sci-biology/embassy-hmmer/ChangeLog
+++ b/sci-biology/embassy-hmmer/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-hmmer
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.35 2015/03/28 18:02:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.36 2015/06/21 09:05:41 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-hmmer-2.3.2.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-hmmer-2.3.2-r3.ebuild,
   embassy-hmmer-2.3.2.650.ebuild:
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
index a274f84f59ec..784f138742ab 100644
--- a/sci-biology/embassy-hmmer/Manifest
+++ b/sci-biology/embassy-hmmer/Manifest
@@ -1,30 +1,30 @@
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diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
index 78d0c254f25d..90c45632eada 100644
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
+++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
@@ -1,6 +1,12 @@
---- HMMER-2.3.2.650/configure.ac
-+++ HMMER-2.3.2.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 037ca00..f539ab6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +40,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +62,25 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- HMMER-2.3.2.650/src/Makefile.am
-+++ HMMER-2.3.2.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index dc789bc..5a8c38e 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,7 +91,7 @@
  endif
  
  if ISSHARED
-@@ -67,5 +65,5 @@
+@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog
index 2bf7f0584ea8..b9ccb62a85da 100644
--- a/sci-biology/embassy-iprscan/ChangeLog
+++ b/sci-biology/embassy-iprscan/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-iprscan
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.9 2015/03/28 18:01:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.10 2015/06/21 09:07:32 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-iprscan-4.3.1.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-iprscan-4.3.1-r1.ebuild,
   embassy-iprscan-4.3.1.650.ebuild:
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
index 91a255a7a273..0c5d01a5db88 100644
--- a/sci-biology/embassy-iprscan/Manifest
+++ b/sci-biology/embassy-iprscan/Manifest
@@ -1,30 +1,30 @@
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diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
index 955005d51211..8c8a1060e30f 100644
--- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -1,6 +1,13 @@
---- IPRSCAN-4.3.1.650/configure.ac
-+++ IPRSCAN-4.3.1.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 9052ca5..c12c268 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +41,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +63,34 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- IPRSCAN-4.3.1.650/src/Makefile.am
-+++ IPRSCAN-4.3.1.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 0afc96a..904b41a 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,17 +101,10 @@
  endif
  
  if ISSHARED
-@@ -58,5 +56,5 @@
+@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
 -        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
 +        -lajax $(NLADD) $(XLIB)
  endif
---- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am
-+++ IPRSCAN-4.3.1.650/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog
index 317e164226ef..c5ddb1ff5eab 100644
--- a/sci-biology/embassy-meme/ChangeLog
+++ b/sci-biology/embassy-meme/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-meme
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.23 2015/03/28 18:00:56 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.24 2015/06/21 09:09:22 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-meme-4.7.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-meme-4.7.650.ebuild:
   Clean global scope
diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
index ce6970d62d64..2d79c474cd64 100644
--- a/sci-biology/embassy-meme/Manifest
+++ b/sci-biology/embassy-meme/Manifest
@@ -1,27 +1,27 @@
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+AUX embassy-meme-4.7.650_fix-build-system.patch 2860 SHA256 928eb90afbc7b70f69fd4bb7f1090bbd4ea2bd3d7a286b56c947dd481156b5b6 SHA512 c44b219c75e67d17fcfd56145ae3709053bda38b8690141d1e9b846e4e4a9cab135f0dc9c5399e4712cf030ad562dd075f45c393e78157a2c1b92d80903b3d1c WHIRLPOOL 4e93c672ee6026ee7b2e2ff6c8771a375049629f5e24e2e6cf9afa72cced5fc62d21f49c161fb5ffe55f0637ffe14baf78df15c1c95e0a42d3495a1619365141
 DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51
 EBUILD embassy-meme-4.7.650.ebuild 500 SHA256 d030da36a864645226fd35bf0048b6e46fb801355bc01025f8bc50d7a5ac1ffe SHA512 e66161feb869e80c5329d58da59430fd162cba4ac5b986512a9e681f382132f4ceda250c90270461aaddfac14fc2ee1d0e4cec87925e3ecfdc5fd2975f7f744e WHIRLPOOL 1a19ed237cac3bab4a1f07bfed6ec5eeeff2a4086a86724c1d21fda60fa850b609ddb115a702bd6bf39dbad0363c451d420b0919c0406688bdf4db56a9905a89
-MISC ChangeLog 597 SHA256 07aacca9f178d77c2a3b0104edd0be0ef67d56340789af828a7e2ff33bc2a4ef SHA512 be00d17e32f0cbef751036199ae82b0e04616f83c9d050ef3431dfad76342919aefcf7690ce8aa31e2cfd5296506cb3936c1f6bdccd44d23dd7b7cc4708efee2 WHIRLPOOL 2212a36dc27f76393f86857741958ee79207b9f83106deb47423f636f51e7610972490da7efa1c721a13621345a8b2b8692aba340d0eeb2dcc50616da4c80fd8
+MISC ChangeLog 750 SHA256 dd4f3a12304e509ea4abd9caa5a5e1b68b2bc1df56b9c3cd26233de0531fea4a SHA512 0b079723cd9c0a825cae54d654e4ccc7f051242ec7eb399de0265e2ce43960b57d7854825535a2300a0b96ac70d735b6d23fe086a13192108b14addd4f3605c0 WHIRLPOOL af77519eb83320b982ed520d1d2b7a81edf88d4971a731c8964bca1080c2c4a9b4202a1f16addd68bca4893699a08b4419bc504fb34a4e0552d809646f272bd9
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
index 03c42460455e..56f5814e1efa 100644
--- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
+++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
@@ -1,6 +1,12 @@
---- MEME-4.7.650/configure.ac
-+++ MEME-4.7.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 391989f..d921f25 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +40,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +62,25 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- MEME-4.7.650/src/Makefile.am
-+++ MEME-4.7.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1600399..9f28162 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,7 +91,7 @@
  endif
  
  if ISSHARED
-@@ -60,5 +58,5 @@
+@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog
index 3e2233894889..ed526bcdb519 100644
--- a/sci-biology/embassy-mse/ChangeLog
+++ b/sci-biology/embassy-mse/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-mse
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.41 2015/03/28 17:59:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.42 2015/06/21 09:10:58 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-mse-3.0.0.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-mse-1.0.0-r7.ebuild,
   embassy-mse-3.0.0.650.ebuild:
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 6dc11a4a06f8..4e1060aa702d 100644
--- a/sci-biology/embassy-mse/Manifest
+++ b/sci-biology/embassy-mse/Manifest
@@ -1,30 +1,30 @@
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+AUX embassy-mse-3.0.0.650_fix-build-system.patch 4274 SHA256 599b095e98864d4268b5959517c1002b3b591a45d865e42f409eb0059af5168b SHA512 bfb4663a4b38928f765813cc9b5e773ca712c2333c1650d9c78f457307aa450684f77a20c0a087d3795d5b51f059c6f8113e74da35aa78753c1cc666ba583f4b WHIRLPOOL 418dc60bb9cf2023d499eec13b132f1aaab7bd9538ba2bc12f3f19926a25f7e7f0fb3b9b99e80acddfb57a4762aba5c90e413ffe5c8aa05d593d1309ecc28db8
 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
 DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90
 DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b
 EBUILD embassy-mse-1.0.0-r6.ebuild 598 SHA256 40ae8e6cb04fd32fcaa7d93c4a9b247d555f76fff212fb5b0ce2228ec46e4465 SHA512 fc8c501160f9d93eee5e5f72b2a3421fc8a290b66da5802f973c12102334050c8afb9727fd1a1598a1d8cefc6a05db926c1cd63ea94c82f6108959fa552989eb WHIRLPOOL e8368ff3f0e0d5f768964d84cc3c4934ecf6f45060a52e161030a93c160c88b848b0fa659ef84d10e2767f15b35dda53c263524cb3169d6b94f3adcda1d6c304
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diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
index 8b2f0574e3b0..c1095b266d60 100644
--- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
@@ -1,6 +1,27 @@
---- MSE-3.0.0.650/configure.ac
-+++ MSE-3.0.0.650/configure.ac
-@@ -635,33 +635,6 @@
+ ckit/Makefile.am       |  2 +-
+ configure.ac           | 67 +++++++++++---------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++---
+ 4 files changed, 18 insertions(+), 59 deletions(-)
+
+diff --git a/ckit/Makefile.am b/ckit/Makefile.am
+index f87b131..a670d2b 100644
+--- a/ckit/Makefile.am
++++ b/ckit/Makefile.am
+@@ -2,7 +2,7 @@
+ 
+ lib_LTLIBRARIES = libckit.la
+ 
+-AM_CPPFLAGS = -I../h
++AM_CPPFLAGS = -I$(top_srcdir)/h
+ 
+ CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
+ seqspec.c ttyinterface.c nextseqentry.c \
+diff --git a/configure.ac b/configure.ac
+index a20d488..eb208bf 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +55,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,19 +77,21 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-@@ -1000,17 +963,13 @@
+@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"],
  
  
  
@@ -93,9 +116,20 @@
  
  
  
---- MSE-3.0.0.650/src/Makefile.am
-+++ MSE-3.0.0.650/src/Makefile.am
-@@ -18,9 +18,7 @@
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index b44632a..84e89b5 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -106,28 +140,10 @@
  endif
  
  if ISSHARED
-@@ -60,5 +58,5 @@
+@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \
  	$(XLIB)
  else
  LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
 -	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
 +	-lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB)
  endif
---- MSE-3.0.0.650/ckit/Makefile.am
-+++ MSE-3.0.0.650/ckit/Makefile.am
-@@ -2,7 +2,7 @@
- 
- lib_LTLIBRARIES = libckit.la
- 
--AM_CPPFLAGS = -I../h
-+AM_CPPFLAGS = -I$(top_srcdir)/h
- 
- CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
- seqspec.c ttyinterface.c nextseqentry.c \
---- MSE-3.0.0.650/emboss_acd/Makefile.am
-+++ MSE-3.0.0.650/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog
index 81bc2d6382c4..9550a755c8be 100644
--- a/sci-biology/embassy-phylipnew/ChangeLog
+++ b/sci-biology/embassy-phylipnew/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-phylipnew
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.17 2015/03/28 17:58:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.18 2015/06/21 09:12:29 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-phylipnew-3.69.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-phylipnew-3.68.ebuild,
   embassy-phylipnew-3.69.650.ebuild:
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
index 3e77749d83e3..037d0e570be2 100644
--- a/sci-biology/embassy-phylipnew/Manifest
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -1,30 +1,30 @@
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+AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 SHA256 26aad2bc72f89444dffdd301cfd4f50ba582b10082f21153e601c6812075ba86 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249 WHIRLPOOL de7d91731115bca913a65a8f4a44d863433338ea4e5acb7f6a9fefca9a185325b18888d8339d180a49ecb7dfeb91f120a7c7188fe23f340dd21aeb8b3940458e
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diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
index e0efb74bd79e..1cba944094a2 100644
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
@@ -1,6 +1,13 @@
---- PHYLIPNEW-3.69.650/configure.ac
-+++ PHYLIPNEW-3.69.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  7 ++-----
+ 3 files changed, 10 insertions(+), 48 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index e5bfaf1..09ed517 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +41,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -781,21 +754,6 @@
+@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +63,34 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -918,6 +876,11 @@
+@@ -918,6 +876,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- PHYLIPNEW-3.69.650/src/Makefile.am
-+++ PHYLIPNEW-3.69.650/src/Makefile.am
-@@ -16,10 +16,7 @@
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1883ce9..fb1787f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -82,17 +102,10 @@
  endif
  
  if ISSHARED
-@@ -120,5 +117,5 @@
+@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	../../../plplot/libeplplot.la $(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
 -        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
 +        -lajax $(NLADD) $(XLIB)
  endif
---- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am
-+++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog
index 595355846470..57c35be3208a 100644
--- a/sci-biology/embassy-signature/ChangeLog
+++ b/sci-biology/embassy-signature/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-signature
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.24 2015/03/29 08:44:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.25 2015/06/21 09:13:51 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-signature-0.1.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   29 Mar 2015; Justin Lecher <jlec@gentoo.org>
   -embassy-signature-0.1.0-r4.ebuild:
diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest
index 0d8bb05ee43d..d1033084f159 100644
--- a/sci-biology/embassy-signature/Manifest
+++ b/sci-biology/embassy-signature/Manifest
@@ -1,30 +1,30 @@
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diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
index 5197c6422f5a..32e4d684cbb3 100644
--- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
@@ -1,6 +1,12 @@
---- SIGNATURE-0.1.650/configure.ac
-+++ SIGNATURE-0.1.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 2f5ddd0..827543f 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +40,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +62,25 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- SIGNATURE-0.1.650/src/Makefile.am
-+++ SIGNATURE-0.1.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index d77e43c..849f17a 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,7 +91,7 @@
  endif
  
  if ISSHARED
-@@ -68,5 +66,5 @@
+@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog
index d19f8e6ffdc2..c7e3b80ce5ff 100644
--- a/sci-biology/embassy-structure/ChangeLog
+++ b/sci-biology/embassy-structure/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-structure
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.24 2015/03/28 17:57:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.25 2015/06/21 09:15:24 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-structure-0.1.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org>
   -embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.650.ebuild:
diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest
index 7d78d9fa4c1d..89f404195bbb 100644
--- a/sci-biology/embassy-structure/Manifest
+++ b/sci-biology/embassy-structure/Manifest
@@ -1,30 +1,30 @@
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diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
index c87eefde11ce..bdd9e37714e4 100644
--- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
+++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
@@ -1,6 +1,12 @@
---- STRUCTURE-0.1.650/configure.ac
-+++ STRUCTURE-0.1.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  6 ++----
+ 2 files changed, 9 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index ee482ef..e4af4b1 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +40,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +62,25 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- STRUCTURE-0.1.650/src/Makefile.am
-+++ STRUCTURE-0.1.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 81ade5d..2ed0d14 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,7 +91,7 @@
  endif
  
  if ISSHARED
-@@ -66,5 +64,5 @@
+@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog
index 4f7b2d168b75..a4bb74826f1c 100644
--- a/sci-biology/embassy-topo/ChangeLog
+++ b/sci-biology/embassy-topo/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-topo
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.34 2015/03/28 17:56:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.35 2015/06/21 09:16:49 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-topo-2.0.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-topo-1.0.0-r6.ebuild,
   embassy-topo-2.0.650.ebuild:
diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest
index da7ef761df6b..97a041b11d87 100644
--- a/sci-biology/embassy-topo/Manifest
+++ b/sci-biology/embassy-topo/Manifest
@@ -1,30 +1,30 @@
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+AUX embassy-topo-2.0.650_fix-build-system.patch 3167 SHA256 d78bcacee455ab12fdb482fa760eb89716da3bac9dbf5ace0f9bba37f2585dbf SHA512 bacff621e9d80d39a4e415736e1524cf69dd86b0253f65fb52ad2dda200cafe8e14af296897c3f695bbe360f2a56862a40dec6b8b0d0e597310f065e191ae770 WHIRLPOOL 09ffc786288a0b428f349cf74973729a9dea8d8ed2078897538b97b59ef41cd48053e0763c6665310a770c6410b28726fe9c09b0ada9543d6fd8054b1e99b24f
 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
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diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
index 7ddda05cb62d..3c37879de8c8 100644
--- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
+++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
@@ -1,6 +1,13 @@
---- TOPO-2.0.650/configure.ac
-+++ TOPO-2.0.650/configure.ac
-@@ -635,33 +635,6 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  6 ++----
+ 3 files changed, 10 insertions(+), 47 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 8eeb8ca..4fd28ac 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +41,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
+@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +63,34 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,11 @@
+@@ -874,6 +832,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- TOPO-2.0.650/src/Makefile.am
-+++ TOPO-2.0.650/src/Makefile.am
-@@ -17,9 +17,7 @@
+diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- a/emboss_acd/Makefile.am
++++ b/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1cdb0b1..0e86a4b 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,17 +101,10 @@
  endif
  
  if ISSHARED
-@@ -60,5 +58,5 @@
+@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
  	$(XLIB)
  else
  LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
 -        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
 +        -lajax $(NLADD) $(XLIB)
  endif
---- TOPO-2.0.650/emboss_acd/Makefile.am
-+++ TOPO-2.0.650/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog
index 2133af5a45c0..ec10ac284092 100644
--- a/sci-biology/embassy-vienna/ChangeLog
+++ b/sci-biology/embassy-vienna/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/embassy-vienna
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.12 2015/03/28 17:55:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.13 2015/06/21 09:18:26 jlec Exp $
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org>
+  files/embassy-vienna-1.7.2.650_fix-build-system.patch:
+  Update buildsystem for latest plplot, bug #552492
 
   28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-vienna-1.7.2-r1.ebuild,
   embassy-vienna-1.7.2.650.ebuild:
diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest
index 359e45c5ce2b..b7f29a635256 100644
--- a/sci-biology/embassy-vienna/Manifest
+++ b/sci-biology/embassy-vienna/Manifest
@@ -1,30 +1,30 @@
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diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
index c9ece691229c..5ce365ed5497 100644
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
@@ -1,6 +1,12 @@
---- VIENNA-1.7.2.650/configure.ac
-+++ VIENNA-1.7.2.650/configure.ac
-@@ -649,33 +649,6 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  7 +++----
+ 2 files changed, 10 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f5a4ecf..bbe0743 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -649,33 +649,6 @@ AS_CASE([${host_os}],
  
  
  
@@ -34,7 +40,7 @@
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -751,21 +724,6 @@
+@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL
  
  
  
@@ -56,21 +62,25 @@
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -888,6 +846,11 @@
+@@ -888,6 +846,13 @@ 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([PLPLOT], [plplotd])
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
 +])
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- VIENNA-1.7.2.650/src/Makefile.am
-+++ VIENNA-1.7.2.650/src/Makefile.am
-@@ -32,9 +32,7 @@
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1f5b756..e178914 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -81,7 +91,7 @@
  endif
  
  if ISSHARED
-@@ -87,6 +85,7 @@
+@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF)
  endif
  
  liboviennarna_la_LDFLAGS = $(LINKFLAGS)
@@ -89,7 +99,7 @@
  
  ovrnaalifold_SOURCES = vrnaalifold.c
  ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
-@@ -119,5 +118,5 @@
+@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \
  	$(XLIB)
  else
  LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
author	Justin Lecher <jlec@gentoo.org>	2015-06-21 09:18:27 +0000
committer	Justin Lecher <jlec@gentoo.org>	2015-06-21 09:18:27 +0000
commit	609992e8e730a2f883e43399c2d06406102a08a6 (patch)
tree	eda0114aa3c8bf435aa0f5976a184f77288524f7 /sci-biology
parent	Drop unneeded -ppc. (diff)
download	historical-609992e8e730a2f883e43399c2d06406102a08a6.tar.gz historical-609992e8e730a2f883e43399c2d06406102a08a6.tar.bz2 historical-609992e8e730a2f883e43399c2d06406102a08a6.zip