Version Bump, test cases fixed

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

diff --git a/sci-chemistry/molrep/ChangeLog b/sci-chemistry/molrep/ChangeLog
index 7816b64c28c47780d179161ee7ed9e806c10024e..3446e19445a73e2fbc4da054998e049939887c0b 100644 (file)
--- a/sci-chemistry/molrep/ChangeLog
+++ b/sci-chemistry/molrep/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/molrep
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/ChangeLog,v 1.4 2010/04/25 11:29:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/ChangeLog,v 1.5 2010/06/15 10:51:43 jlec Exp $
+
+*molrep-11.0.00 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org>
+  +files/11.0.00-respect-FLAGS.patch, +molrep-11.0.00.ebuild,
+  +files/11.0.00-test.patch:
+  Version Bump, test cases fixed
 
 *molrep-10.2.38 (12 Mar 2010)
 

diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
index 0580d4d4981bfed42e7aea1217b17a4bd7131f54..f3447e106bd486942b4928d378a57608dbad70f2 100644 (file)
--- a/sci-chemistry/molrep/Manifest
+++ b/sci-chemistry/molrep/Manifest
@@ -2,16 +2,20 @@
 Hash: SHA1
 
 AUX 10.2.35-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
+AUX 11.0.00-respect-FLAGS.patch 364 RMD160 b364dfd896cd954740960eb32c15f47e9c2cdffd SHA1 50e945f5f6f8b0785547c2bebeea26f93421bb39 SHA256 04a8fbd74b3f9280fbb7d5abe701cee5f59901c258afdfc16b4d37809200c461
+AUX 11.0.00-test.patch 5153 RMD160 70dabd2f772cbcad4c8cd1ea617838a6a1b61f55 SHA1 b3b66bcb1661a1fcd3c7700310dda4a1642293c3 SHA256 f057baee3a42a3a517199c039018d8042d4da098976636950871d650e6d5acd1
 DIST molrep-10.2.35.tar.gz 6811806 RMD160 d57247bd5b0b56ab37d8a8f165c965061fab0ddd SHA1 4c93f4d4879c678e010741d2a0f06fa4f07e5ccd SHA256 ab51428c6c96ea03ced48d87236e163e7f24ee9ed03d012467188bc91c991ed9
 DIST molrep-10.2.38.tar.gz 3602579 RMD160 e7431eebef2d38561e2fd50abd1151156f2b3041 SHA1 62607b0d66b43ef1fc8ea03b2bacf8f9c4860193 SHA256 ef1a54f8e51809047cbdffd0b7af4744630b53deb32bcdc6aedb7fa051cb21f9
+DIST molrep-11.0.00.tar.gz 3654740 RMD160 23730cefb41c7660a2b87aa8e934bb341239c07f SHA1 8bf56dca661db884ed8710705b5ba981c95bf4fa SHA256 2da9e0bec4e007ffeccc110ee03a908e85cfc960ce830b46d759128c9faf80ea
 EBUILD molrep-10.2.35.ebuild 995 RMD160 add805cce8c5da8bc4f8a97d6a0e29cabcc89ef1 SHA1 de49fa951e58a900ebbbe3aaede5b10b1a950f22 SHA256 76a29084ca80654704354401f8c2bdfbfcf5099baf47082ba41e59fc4fa7f75a
 EBUILD molrep-10.2.38.ebuild 960 RMD160 34220d5fce746c2f9394996e285cd3136c2f9fb3 SHA1 94c74fbfd73958748f238b97994357b1ff9a93ac SHA256 f0512d708faac02dad2995750bd90e796fe14c08a38262e619e3c97135c67438
-MISC ChangeLog 620 RMD160 2bddfb557f216c8541e3e2a89606989397bb02ec SHA1 65fa91dca2a2843221dee0722b4c2fcf63132675 SHA256 842945fce9a0a40fa12149c1d5b41a66512a41a44365691e6a2b15dd30362028
+EBUILD molrep-11.0.00.ebuild 1190 RMD160 797ffa435f35d423db11a710c6a7776f002a33ce SHA1 b6f9fa6311352a33bd5ef04a651800b439ffe16b SHA256 bdf36aeba457c70a1bc5af888f289d3d87bb69981d4d918290993758ddd14e6d
+MISC ChangeLog 823 RMD160 d78bef945daca6321f60cba54c6811eaa6726b3e SHA1 9a0a5680d275bc733784098b86d430e53c8a216e SHA256 8fd7494bcced5a8b1384e39b3edbfe56b885956a6e05124359b446a5cdc4e537
 MISC metadata.xml 226 RMD160 0355d90bd8d1c106a19b136045ebdf970a0a2485 SHA1 1db0b2a470657641079d6613829df49a5c043ed6 SHA256 094a3ac740c81b9afbff3c855ba93cc20a593cad2392f6f4404715608a836fa1
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkvUJ6UACgkQgAnW8HDreRZapACfXLQHZR9GnLZ/3BI2Brgk2E79
-kEkAn0/fSTDVzQh+HlNIcb/aeqnYSb20
-=D7/y
+iEYEARECAAYFAkwXW0kACgkQgAnW8HDreRZUCACgtvosVIAq4Ys7auueMWT5TqVl
+RQ4An2Zw6ac/wY/o5MZPoWSB1IteVijl
+=gcMO
 -----END PGP SIGNATURE-----

diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
new file mode 100644 (file)
index 0000000..c18b9a1
--- /dev/null
+++ b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch
@@ -0,0 +1,12 @@
+diff --git a/src/makefile b/src/makefile
+index 30d0de7..10dd68f 100755
+--- a/src/makefile
++++ b/src/makefile
+@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f
+       $(MR_FORT) -c molrep_dummy.f 
+ 
+ molrep: $(OBJS)
+-      $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
++      $(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
+ 
+ # --------------------------------

diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch
new file mode 100644 (file)
index 0000000..d90cfb8
--- /dev/null
+++ b/sci-chemistry/molrep/files/11.0.00-test.patch
@@ -0,0 +1,191 @@
+diff --git a/molrep_check/em.bat b/molrep_check/em.bat
+index 2f0f992..96ddd75 100755
+--- a/molrep_check/em.bat
++++ b/molrep_check/em.bat
+@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
+ # --------------------------------
+ _NMON  6
+ stop
++echo $?
++[[ $? ]] || exit 1
+ # --------------------------------
+ #
+ # 2. Atomic model --> EM map
+@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
+ _NMON  6
+ _prf  y
+ stop
++[[ $? ]] || exit 1
+ # --------------------------------
+ #
+ # 3. Atomic model --> EM map
+@@ -36,6 +39,7 @@ _ncs  322
+ _centre  0.500 0.490 0.490
+ _angles  0.0 0.0 90.0  
+ stop
++[[ $? ]] || exit 1
+ # --------------------------------
+ #
+ cp out/molrep.pdb hexamer.pdb
+@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop
+ # --------------------------------
+ _DOM s
+ stop
++[[ $? ]] || exit 1
+ # --------------------------------
+ #
+ # 5. EM --> X-ray     
+@@ -60,6 +65,7 @@ stop
+ $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
+ # --------------------------------
+ stop
++[[ $? ]] || exit 1
+ # --------------------------------
+ #
+ # 6. Placing  the model to a particular orientation and position.
+@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif  -m ../em/pel.map -po out/ -ps scr/ -i <<stop
+ _fun  s
+ _file_t ../em/tab
+ stop
++[[ $? ]] || exit 1
+ #==========================================
+diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat
+index 284a4cd..6e00695 100755
+--- a/molrep_check/mr.bat
++++ b/molrep_check/mr.bat
+@@ -10,6 +10,7 @@
+ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop
+ # --------------------------------
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -26,6 +27,7 @@ _nmon   2
+ _COMPL  .5
+ _SIM    .7
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod
+ # --------------------------------
+ _NP    3
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i
+ _NMON   2
+ _NP     3
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -85,6 +89,7 @@ _NPT    3
+ _NPTD   3
+ _DYAD   D
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -103,6 +108,7 @@ _NP    3
+ _NPT   10
+ _NMR   3
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -118,6 +124,7 @@ _PRF Y
+ _compl 1.
+ _sim   .2
+ stop
++[[ $? ]] || exit 1
+ #
+ # =================================================================
+ #
+@@ -136,6 +143,7 @@ _ph   PH
+ _fom  FOM
+ #
+ stop
++[[ $? ]] || exit 1
+ # =================================================================
+ #
+ #   9. use sequence
+@@ -145,6 +153,7 @@ stop
+ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop 
+ # --------------------------------
+ stop
++[[ $? ]] || exit 1
+ # =================================================================
+ #
+ #   10. Locked RF
+@@ -157,6 +166,7 @@ _lock y
+ _file_tsrf ../data/srf.tab
+ _nsrf 1
+ stop
++[[ $? ]] || exit 1
+ # =================================================================
+ #
+ #   11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and 
+@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p
+ _self a
+ _nsrf 1
+ stop
++[[ $? ]] || exit 1
+ # =================================================================
+ #
+ #   12.  use pst
+@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i
+ # --------------------------------
+ #
+ stop
++[[ $? ]] || exit 1
+ # =================================================================
+ #
+ #   13. space group check
+@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i
+ # --------------------------------
+ _sg all
+ #
+-stop
++s[[ $? ]] || exit 1
++top
+ # ==========================================================
+ #  
+ #  14. Example for finding HA position by MR solution.
+@@ -206,6 +219,7 @@ _SIGFD  SIGFD3
+ #
+ _FUN   d
+ stop
++[[ $? ]] || exit 1
+ # ==========================================================
+ #  
+ #  15. Example for HA search by multi-copy search
+@@ -225,6 +239,7 @@ _diff h
+ _dyad y
+ _nmon 4
+ stop
++[[ $? ]] || exit 1
+ # ==========================================================
+ #  
+ #  16. Example HA for search by translation function
+@@ -242,6 +257,7 @@ _FUN  t
+ _diff  h
+ _nmon  4
+ stop
++[[ $? ]] || exit 1
+ # ==========================================================
+ #  
+ #  17. Example for Self RF for Heavy Atom structure in derivative.
+@@ -258,4 +274,5 @@ _SIGFD  SIGFD3
+ _FUN  r
+ _diff  h
+ stop
++[[ $? ]] || exit 1
+ # ==========================================================

diff --git a/sci-chemistry/molrep/molrep-11.0.00.ebuild b/sci-chemistry/molrep/molrep-11.0.00.ebuild
new file mode 100644 (file)
index 0000000..8e0295c
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-11.0.00.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/molrep-11.0.00.ebuild,v 1.1 2010/06/15 10:51:43 jlec Exp $
+
+EAPI="3"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+       >=sci-libs/ccp4-libs-6.1.3
+       sci-libs/mmdb
+       virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+       epatch "${FILESDIR}"/${PV}-respect-FLAGS.patch
+       epatch "${FILESDIR}"/${PV}-test.patch
+}
+
+src_compile() {
+       cd "${S}"/src
+       emake clean || die
+       emake \
+               MR_FORT="$(tc-getFC) ${FFLAGS}" \
+               FFLAGS="${FFLAGS}" \
+               LDFLAGS="${LDFLAGS}" \
+               MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c -lmmdb -lccif -llapack -lstdc++ -lm" \
+               || die
+}
+
+src_test() {
+       export MR_TEST="${S}/bin/"
+       cd "${S}"/molrep_check/work
+       mkdir out scr
+       cp ../*.bat .
+       bash em.bat || die
+       bash mr.bat || die
+}
+
+src_install() {
+       dobin bin/${PN} || die
+       dodoc readme doc/${PN}.rtf || die
+}