sci-chemistry/ambertools update but still problems

6 files changed, 104 insertions, 12 deletions

diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 492da0ce5..edda052d0 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1,5 +1,7 @@
-AUX 1.2-Makefile_at.patch 830 RMD160 a6e007e5f86ea244e95b2e24955f487d2e5c4f72 SHA1 50c3d7cd3691a2d9e189f0f0c8138dbaf7111c3c SHA256 ed157fad8d36c35636ea2377723b1623669434c8ddac3c050beeea85f90cc178
-AUX 1.2-configure_at.patch 852 RMD160 57bd7b529c3be0ed5c94856f1603d5288e1fd338 SHA1 a9d7d003f6926cc79289d6924d44a5488a85f3d4 SHA256 84b219694b85edf6ed40546e769666e67844da1b68f44cfdae6c4bbf484bc627
+AUX 1.2-Makefile_at-f2c.patch 1169 RMD160 114ed61db0bc5759cdce0501252ccf68525f05c8 SHA1 ce3742a65ddb3472d38ac3265bf9ae0de64ef21c SHA256 6d1f4de9d7a7e8826f5acbf6ee4aee5c0dd10596e25e51b229c7975e6dc71bfa
+AUX 1.2-Makefile_at.patch 830 RMD160 610311006a6d5ed95aedb81ecf1bb849c1dd3bdd SHA1 34d7e60d33196b0f3abc357ee965a179ec1c0581 SHA256 bbd7f96be1638d55c8171077e21474c1a98a300c03e367b18bdc8555e40e9745
+AUX 1.2-configure_at.patch 853 RMD160 cd50792ce60f2537d121ebd8531b3bb70539ba95 SHA1 d632b90a7c525e1b7636d713a119316a38e3903e SHA256 58c009dae95aa4f60b2f6423f3794e4c8491f423f2df2d30e9606f0b2842d458
+AUX 1.2-f2c.patch 1012 RMD160 78e0c5a5320f151e031f5c546d88292ece0852c8 SHA1 5a2f98686e5e0444ab0505cb4c0cba97ac0f4332 SHA256 f857a9b972e54803a5684511708a273c0c895a41a4dbbfac9c168900968d618d
 DIST AmberTools-1.2.tar.bz2 50621801 RMD160 01dd22dd86b90148111dc0616964384dfeda467c SHA1 001db6742fdbf0f0f8c862d1b08a59ea3da0b684 SHA256 1630e0c0135de05441226a08a5f60d861faeb7a06f5d1a4bc38e9eeff4b2f991
-EBUILD ambertools-1.2.ebuild 2030 RMD160 b4428ce5a569b03fdaa4e8cc9f36426de3ba304e SHA1 014451ef55d5060a941ee59476d61e149bd0a81b SHA256 e8479895c644cd3efc26f1daeb0ddd88c3adf31dcd92448abfa0cf69e57d9d50
+EBUILD ambertools-1.2.ebuild 2374 RMD160 58858e7c056bda4c973e4f227dcacb3427203c8e SHA1 cac33fc2cba08464d18d188d54d8263b03c69953 SHA256 a8c50224588cf987e1f4aa5148f6bbfb78d57b0af4d695753959585024893468
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/ambertools/ambertools-1.2.ebuild b/sci-chemistry/ambertools/ambertools-1.2.ebuild
index 6275b486d..15e5e2741 100644
--- a/sci-chemistry/ambertools/ambertools-1.2.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.2.ebuild
@@ -18,8 +18,16 @@ KEYWORDS="~amd64 ~x86"
 IUSE="mpi openmp scalapack X"
 RESTRICT="fetch"
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
+RDEPEND="virtual/cblas
+	sci-libs/clapack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
 S="${WORKDIR}"/amber10
 
 pkg_nofetch() {
@@ -41,14 +49,18 @@ pkg_setup() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-configure_at.patch
-	epatch "${FILESDIR}"/${PV}-Makefile_at.patch
+	epatch "${FILESDIR}"/${PV}-configure_at.patch \
+		"${FILESDIR}"/${PV}-Makefile_at.patch 
+#		"${FILESDIR}"/${PV}-Makefile_at-f2c.patch 
+#		"${FILESDIR}"/${PV}-f2c.patch
+	cd src && rm -rf byacc c9x-complex carpack cblas cifparse clapack mopac6 netcdf reduce ucpp-1.3
+# f2c
 }
 
 src_configure() {
 	cd src
 	sed -e "s:\\\\\$(LIBDIR)/arpack.a:/usr/$(get_libdir)/libarpack.a:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/liblapack.a:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/libclapack.a:g" \
 		-e "s:\\\\\$(LIBDIR)/blas.a:/usr/$(get_libdir)/libcblas.a:g" \
 		-e "s:\\\\\$(LIBDIR)/f2c.a:/usr/$(get_libdir)/libf2c.a:g" \
 		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
diff --git a/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch b/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch
new file mode 100644
index 000000000..a5da04962
--- /dev/null
+++ b/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch
@@ -0,0 +1,42 @@
+--- src/Makefile_at	2008-07-11 00:09:01.000000000 +0200
++++ src/Makefile_at.new	2009-03-25 15:35:51.000000000 +0100
+@@ -5,29 +5,29 @@
+ install:
+ 	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && make $(UCPP) )
+-	(cd byacc && make install )
+-	(cd carpack && make install );
+-	(cd clapack && make $(LAPACK) )
+-	(cd cblas && make $(BLAS) )
+-	(cd f2c &&  make $(F2C)  )
+-	(cd c9x-complex && make $(C9XCOMPLEX) )
++#	(cd ucpp-1.3 && make $(UCPP) )
++#	(cd byacc && make install )
++#	(cd carpack && make install );
++#	(cd clapack && make $(LAPACK) )
++#	(cd cblas && make $(BLAS) )
++#	(cd f2c &&  make $(F2C)  )
++#	(cd c9x-complex && make $(C9XCOMPLEX) )
+ 
+ #	nab, leap, and sleap:
+-	(cd cifparse && make install )
++#	(cd cifparse && make install )
+ 	(cd nab && make install )
+ 	(cd nss && make install )
+ 
+ #	antechamber:
+ 	(cd antechamber && make install )
+-	(cd mopac6/src && make $(G77) )
++#	(cd mopac6/src && make $(G77) )
+ 	(cd resp && make $(G77) )
+ 
+ #   ptraj:
+ 	(cd ptraj && make install )
+ 
+ #   miscellaneous:
+-	(cd reduce && make install )
++#	(cd reduce && make install )
+ 
+ #   leap and gleap:
+ 	(cd leap && make install )
diff --git a/sci-chemistry/ambertools/files/1.2-Makefile_at.patch b/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
index 36a9b75d3..139f04e8c 100644
--- a/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
+++ b/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
@@ -1,6 +1,6 @@
 --- src/Makefile_at	2008-07-11 00:09:01.000000000 +0200
-+++ src/Makefile_at.new	2009-03-22 20:44:20.818437912 +0100
-@@ -5,29 +5,19 @@
++++ src/Makefile_at.new	2009-03-25 19:05:35.000000000 +0100
+@@ -5,29 +5,20 @@
  install:
  	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
  #	utility routines and libraries:
@@ -9,7 +9,7 @@
 -	(cd carpack && make install );
 -	(cd clapack && make $(LAPACK) )
 -	(cd cblas && make $(BLAS) )
--	(cd f2c &&  make $(F2C)  )
+ 	(cd f2c &&  make $(F2C)  )
 -	(cd c9x-complex && make $(C9XCOMPLEX) )
  
  #	nab, leap, and sleap:
diff --git a/sci-chemistry/ambertools/files/1.2-configure_at.patch b/sci-chemistry/ambertools/files/1.2-configure_at.patch
index 69e902131..9c409462f 100644
--- a/sci-chemistry/ambertools/files/1.2-configure_at.patch
+++ b/sci-chemistry/ambertools/files/1.2-configure_at.patch
@@ -23,7 +23,7 @@
  
  LEX=   $lex
 -YACC=  \$(BINDIR)/yacc
-+YACC=  /usr/bin/yacc
++YACC=  /usr/bin/byacc
  AR=    ar rv
  M4=    $m4
  RANLIB=$ranlib
diff --git a/sci-chemistry/ambertools/files/1.2-f2c.patch b/sci-chemistry/ambertools/files/1.2-f2c.patch
new file mode 100644
index 000000000..a77d7f60c
--- /dev/null
+++ b/sci-chemistry/ambertools/files/1.2-f2c.patch
@@ -0,0 +1,36 @@
+diff -arNu src/nab.orig/dmcsrch.c src/nab/dmcsrch.c
+--- src/nab.orig/dmcsrch.c	2009-03-24 22:35:01.000000000 +0100
++++ src/nab/dmcsrch.c	2009-03-24 22:35:05.000000000 +0100
+@@ -3,7 +3,7 @@
+ 	-lf2c -lm   (in that order)

+ */

+ 

+-#include "../f2c/f2c.h"

++#include <f2c.h>

+ 

+ /*     Original version from Jorge Nocedal, slightly modified */

+ /*     by Istvan Kolossvary to link to libXMIN. See CIK comments. */

+diff -arNu src/nab.orig/ms.c src/nab/ms.c
+--- src/nab.orig/ms.c	2009-03-24 22:35:01.000000000 +0100
++++ src/nab/ms.c	2009-03-24 22:35:09.000000000 +0100
+@@ -3,7 +3,7 @@
+ 	-lf2c -lm   (in that order)

+ */

+ 

+-#include "../f2c/f2c.h"

++#include <f2c.h>

+ 

+ /* Common Block Declarations */

+ 

+diff -arNu src/nab.orig/nmode.c src/nab/nmode.c
+--- src/nab.orig/nmode.c	2009-03-24 22:35:01.000000000 +0100
++++ src/nab/nmode.c	2009-03-24 22:35:04.000000000 +0100
+@@ -7,7 +7,7 @@
+ #else
+ #  include <complex.h>
+ #endif
+-#include "../f2c/f2c.h"
++#include <f2c.h>
+ 
+ #include "nab.h"
+ #include "memutil.h"