proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

8 files changed, 406 insertions, 0 deletions

diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
new file mode 100644
index 000000000000..7206bd5555b8
--- /dev/null
+++ b/sci-chemistry/molrep/Manifest
@@ -0,0 +1,2 @@
+DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce
+DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
new file mode 100644
index 000000000000..d81ec793b510
--- /dev/null
+++ b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch
@@ -0,0 +1,61 @@
+--- src/makefile	2009-02-27 16:51:46.492890717 +0100
++++ src/makefile.new	2009-02-27 16:52:18.295619642 +0100
+@@ -5,8 +5,8 @@
+ 
+ BIN = $(MOLREP)/bin
+ 
+-OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
+-OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
++OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
++OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
+ 
+ 
+ all: molrep
+@@ -19,31 +19,31 @@
+ # -----------------------------
+ 
+ molrep.o: molrep.f 
+-	$(MR_FORT) -c molrep.f 
++	$(MR_FORT) $(FFLAGS) -c molrep.f
+ molrep1.o: molrep1.f 
+-	$(MR_FORT) -c molrep1.f 
++	$(MR_FORT) $(FFLAGS) -c molrep1.f
+ molrep2.o: molrep2.f 
+-	$(MR_FORT) -c molrep2.f 
++	$(MR_FORT) $(FFLAGS) -c molrep2.f
+ molrep3.o: molrep3.f 
+-	$(MR_FORT) -c molrep3.f 
++	$(MR_FORT) $(FFLAGS) -c molrep3.f
+ molrep_prog.o: molrep_prog.f 
+-	$(MR_FORT) -c molrep_prog.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog.f
+ molrep_prog1.o: molrep_prog1.f 
+-	$(MR_FORT) -c molrep_prog1.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f
+ molrep_prog2.o: molrep_prog2.f 
+-	$(MR_FORT) -c molrep_prog2.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f
+ molrep_subr.o: molrep_subr.f  
+-	$(MR_FORT) -c molrep_subr.f 
+-molrep_sym.o: molrep_sym.f  
+-	$(MR_FORT) -c molrep_sym.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_subr.f
++molrep_sym_ccp4.o: molrep_sym.f  
++	$(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f 
+ main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh 
+-	$(MR_FORT) -c main_molrep_mtz.f 
+-molrep_unix.o: molrep_unix.f 
+-	$(MR_FORT) -c molrep_unix.f 
++	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
++molrep_unix_ccp4.o: molrep_unix.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f 
+ molrep_dummy.o: molrep_dummy.f 
+-	$(MR_FORT) -c molrep_dummy.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_dummy.f 
+ 
+ molrep: $(OBJS)
+-	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
++	$(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
+ 
+ # --------------------------------
+
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
index 000000000000..c18b9a1e3f0d
--- /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
index 000000000000..d90cfb8c7b35
--- /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/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch
new file mode 100644
index 000000000000..430629e8dcc1
--- /dev/null
+++ b/sci-chemistry/molrep/files/11.0.03-EOR.patch
@@ -0,0 +1,16 @@
+ src/molrep.f |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/molrep.f b/src/molrep.f
+index eac0cfc..94f74c6 100755
+--- a/src/molrep.f
++++ b/src/molrep.f
+@@ -1257,7 +1257,7 @@ C         CHECK_DENS_FILE( 2 )
+         LEN1 = 1
+         IF(LEN.GT.60) LEN1 = LEN - 59
+         WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') 
+-     *                                 NAME2(LEN11:LEN)
++     *                                 NAME2(LEN1:LEN)
+         CALL MSGDOC(MDoc,LINE)
+ 
+       ENDIF
diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml
new file mode 100644
index 000000000000..ae9ec7c5f6a4
--- /dev/null
+++ b/sci-chemistry/molrep/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild
new file mode 100644
index 000000000000..51ff6cb26524
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-11.0.02.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	>=sci-libs/ccp4-libs-6.1.3
+	sci-libs/mmdb
+	virtual/lapack"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
+		"${FILESDIR}"/11.0.00-test.patch
+}
+
+src_compile() {
+	cd "${S}"/src
+	emake clean
+	emake \
+		MR_FORT="$(tc-getFC) ${FFLAGS}" \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
+}
+
+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() {
+	exeinto /usr/libexec/ccp4/bin/
+	doexe bin/${PN}
+	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
+	dodoc readme doc/${PN}.rtf
+}
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
new file mode 100644
index 000000000000..3a0d7538b481
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	>=sci-libs/ccp4-libs-6.1.3
+	sci-libs/mmdb
+	virtual/lapack"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
+		"${FILESDIR}"/11.0.00-test.patch \
+		"${FILESDIR}"/${PV}-EOR.patch
+	[[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
+}
+
+src_compile() {
+	cd "${S}"/src
+	emake clean
+	emake \
+		MR_FORT="$(tc-getFC) ${FFLAGS}" \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm"
+}
+
+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() {
+	exeinto /usr/libexec/ccp4/bin/
+	doexe bin/${PN}
+	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
+	dodoc readme doc/${PN}.rtf
+}