Pull in Justin Lecher's fixes from the science overlay, except for ARIA.

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

4 files changed, 276 insertions, 6 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index 4e8649e27420..357d0e1dd09c 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.15 2009/07/07 23:26:17 flameeyes Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.16 2009/07/27 06:26:01 dberkholz Exp $
+
+*cns-1.2.1-r1 (27 Jul 2009)
+
+  27 Jul 2009; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/1.2.1-gentoo.patch, +cns-1.2.1-r1.ebuild:
+  Pull in Justin Lecher's fixes from the science overlay, except for ARIA.
 
   07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> cns-1.2.1.ebuild:
   Use elog for fetch error.
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
index a9fd31708be8..2b4ee79ad475 100644
--- a/sci-chemistry/cns/Manifest
+++ b/sci-chemistry/cns/Manifest
@@ -4,23 +4,25 @@ Hash: SHA1
 AUX 1.1-time-length-10.patch 443 RMD160 664ae29ccb2921954ffb14653e4560ed2bef1fa4 SHA1 ca1ddd1535c54bd541570eaf0187eb4c6f638e13 SHA256 73ca56b80588aabd513d6f5171db1217189899e04b5e460a55824eef13c5505a
 AUX 1.2-allow-unknown-architectures.patch 540 RMD160 559f16141025b3d102a316af79ba0ee195846774 SHA1 d168a0413aab5e84ea48f1de5e0a84bc7206fcc7 SHA256 47f398e4c534f01eb64a1c68d477d21a8371707a0977b900d9f2124d3d37243d
 AUX 1.2.1-allow-gcc-openmp.patch 926 RMD160 b8ccec007a717c53ca15731b1b5637bb067d2dda SHA1 b5c876271029e47e180d1dd6d51df51b648f6232 SHA256 8c650b36ef731f7b799397ac9f6abfe9cdf46508df930e7bd3a0f2a0dc2e2275
+AUX 1.2.1-gentoo.patch 2411 RMD160 a82893524541961a9797fd2bb84982e609fda717 SHA1 7d3168a9cf7622923138022a5683aa65b5d5c34d SHA256 58972606d23d87fdeb08c9e37d9d5c536983e5a1ad4647dedd5b283ef67bc52c
 AUX cns_solve_env_sh 7002 RMD160 23aeaddf9fad54fc52d3b6df68564039764802b4 SHA1 1145438aa5325c9229629bcfd3dae283bc960d72 SHA256 e6191df6265ffc02661f196b91b597fac752e85ca37b4bb735b83fd62a13fe0b
 DIST cns_solve_1.1_basic_inputs.tar.gz 5049767 RMD160 eb5686a006d53cf269456eaecd7507842c8a10eb SHA1 255e7c5170168f9e032ef9e84a870eddf176f4ce SHA256 916d86d96159bd945a3b05e26c71af0cc6097234776385630f618fa2641cf3eb
 DIST cns_solve_1.1_data.tar.gz 18770504 RMD160 a18470f31fa6213e817dadf3c3c56231ebce9e63 SHA1 3eaae5ecd1df14412083af8a31a6e3f7b14c4753 SHA256 da59213013b845ca357decfc11337c7dfdb3134bd012c710291c66e8febdbb37
 DIST cns_solve_1.1_test.tar.gz 2852870 RMD160 2f7e7b5ed4e603b2459944a8991829d1361315b5 SHA1 c50587cf3fdfcb1266d13dbd689a9b8b094fb681 SHA256 c5d049596cca4f6985b0b4997f4fa62345d2c111b8fab534918829ade1899a23
-DIST cns_solve_1.21_all-mp.tar.gz 32758988 RMD160 cdcb19a4a5032891ae4ac17ca8ed4ad43747a7f5 SHA1 e06c0d66183eb0933f7b8b3b7fcbfc2661a05bc8 SHA256 b9f7a7593a462e25898e0473100aaba04866af23e4b8b4d1846f0726da2005e1
+DIST cns_solve_1.21_all-mp.tar.gz 32748040 RMD160 0da9c1858e858474a8798149b7692b9e097adc9e SHA1 3ba32a6622b55dfff397b6844e8b8a594124a482 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1
 DIST cns_solve_1.21_all.tar.gz 32739912 RMD160 ab763373923264497d1ccb507cab23b2e1af9826 SHA1 93059805e14f0482cf58755daecc52cf97863215 SHA256 a581c6a0e9e5ffd45f025520959921d7ba91bb5d1e6569f1c81e709bb6f87c81
 DIST cns_solve_1.2_all.tar.gz 30456531 RMD160 45cff57b3f026d730032cfc1c9476880f7cc81ab SHA1 1611ad499746993a9d210e6053e1cdd1553848a7 SHA256 230847d8e00def4b55dda8c50d9148bca11a88ed6bc575e735041c91f8fff064
 EBUILD cns-1.1.ebuild 3605 RMD160 d909804101c942679132d7c37707e3e0f3cf3617 SHA1 b4d9f4f0fd25618e8a85d9a593c3f3e46bee2efa SHA256 81855368f4aa81e479078187e733b10625ec1a0a893c856b5d97022d64af787e
 EBUILD cns-1.2-r1.ebuild 4474 RMD160 4c00d86abde1f2c046eacbe0d0cd1a989222b724 SHA1 30284469ebd2284cebb4eaf309cc7840afe44894 SHA256 105e0688bc6ac038f97a6ed93905ed16ce15350c81ded1870892653972eb1372
+EBUILD cns-1.2.1-r1.ebuild 5484 RMD160 77f475cf3acd63edd0b4de60899e52bcd9cfef60 SHA1 355a956cb00e7e6544654a7cad6c23c1338ef0c6 SHA256 9b582cfa327173a8d5ed321f4c4f4daa0be4f5940b10e12faa2f323a95068998
 EBUILD cns-1.2.1.ebuild 5581 RMD160 266bdf311cc963b8f6974888890897980791655e SHA1 563c412fbc397c71b4a580e4127df56ac8c4d3e3 SHA256 686f7c10b9ca44b0d9869761467ad529994ab86e84a2808efab9e107e08cce3f
 EBUILD cns-1.2.ebuild 3504 RMD160 e3dd53a4fa0a7118f7571e7bca7819d4ad9e39b5 SHA1 926f47b6b27c48c027d903add199d5445e62b13a SHA256 9eecdffa0fbe9fa50b68ea25654aa8b48dda3abc3eec63b21a6f373cdfd2ee19
-MISC ChangeLog 2716 RMD160 d83b68b0831900fd246d3f36bf53a0d0a16dc902 SHA1 e5cf436d684a284d69aa0492148178c08cc8cfd4 SHA256 7a1f101c04ab78ac3814c7dbc4234580c3a542e9931c47a9de41f9dcde46cc51
+MISC ChangeLog 2927 RMD160 85884210fef3b24017b05349ce00135aa8378cfb SHA1 ed41e0fc25e22d295f73796bbfe609c78bafb57e SHA256 2c258599bd0653b95617812f063c3b70a7c1f72c76424d91a43e9feb378b67b0
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
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-=zEI2
+iEYEARECAAYFAkptSIIACgkQXVaO67S1rtu2WwCfbQANlERhL1QLl6/eyh5yMMKn
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diff --git a/sci-chemistry/cns/cns-1.2.1-r1.ebuild b/sci-chemistry/cns/cns-1.2.1-r1.ebuild
new file mode 100644
index 000000000000..006c3c763e8d
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r1.ebuild
@@ -0,0 +1,190 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r1.ebuild,v 1.1 2009/07/27 06:26:01 dberkholz Exp $
+
+EAPI="2"
+
+inherit eutils fortran toolchain-funcs versionator flag-o-matic
+
+MY_PN="${PN}_solve"
+MY_PV="$(delete_version_separator 2)"
+MY_P="${MY_PN}_${MY_PV}"
+
+DESCRIPTION="Crystallography and NMR System"
+HOMEPAGE="http://cns.csb.yale.edu/"
+SRC_URI="${MY_P}_all-mp.tar.gz"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86"
+IUSE="openmp"
+
+RDEPEND="app-shells/tcsh
+	!app-text/dos2unix"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="g77 gfortran"
+
+pkg_nofetch() {
+	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
+	elog "and place these files:"
+	elog ${A}
+	elog "in ${DISTDIR}."
+}
+
+pkg_setup() {
+	fortran_pkg_setup
+
+	if [[ $(tc-getCC)$ == *gcc* ]] &&
+		( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
+		! built_with_use sys-devel/gcc openmp )
+	then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
+		ewarn "Switch CC to an OpenMP capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+
+	append-fflags -fopenmp
+
+	# the code uses Intel-compiler-specific directives
+	epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
+
+	OMPLIB="-lgomp"
+
+	use amd64 && \
+		append-cflags "-DINTEGER='long long int'" && \
+		append-fflags -fdefault-integer-8
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		"${S}"/cns_solve_env
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
+		"${T}"/cns_solve_env_sh
+}
+
+src_compile() {
+	local GLOBALS
+	local MALIGN
+	if [[ ${FORTRANC} = g77 ]]; then
+		GLOBALS="-fno-globals"
+		MALIGN='\$(CNS_MALIGN_I86)'
+	fi
+
+	# Set up the compiler to use
+	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+	ln -s Makefile.header Makefile.header.${FORTRANC} || die
+	popd 2>/dev/null
+
+	# make install really means build, since it's expected to be used in-place
+	emake \
+		CC="$(tc-getCC)" \
+		F77="${FORTRANC}" \
+		LD="${FORTRANC}" \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		g77install \
+		|| die "emake failed"
+
+}
+
+src_test() {
+	# We need to force on g77 manually, because we can't get aliases working
+	# when we source in a -c
+	einfo "Running tests ..."
+	sh -c \
+		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
+		|| die "tests failed"
+	einfo "Displaying test results ..."
+	cat "${S}"/*_g77/test/*.diff-test
+}
+
+src_install() {
+	# Install to locations resembling FHS
+	sed -i \
+		-e "s:${S}:usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT /usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
+		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${S}"/cns_solve_env
+	# I don't entirely understand why the sh version requires a leading /
+	# for CNS_SOLVE and CNS_ROOT, but it does
+	sed -i \
+		-e "s:${S}:/usr:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=/usr:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
+		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
+		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		"${T}"/cns_solve_env_sh
+
+	# Get rid of setup stuff we don't need in the installed script
+	sed -i \
+		-e "83,$ d" \
+		-e "37,46 d" \
+		"${S}"/cns_solve_env
+	sed -i \
+		-e "84,$ d" \
+		-e "39,50 d" \
+		"${T}"/cns_solve_env_sh
+
+	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
+		|| die "install cns_solve failed"
+
+	# Can be run by either cns_solve or cns
+	dosym cns_solve /usr/bin/cns
+
+	# Don't want to install this
+	rm -f "${S}"/*_g77/utils/Makefile
+
+	dobin "${S}"/*_g77/utils/* || die "install utils failed"
+
+	sed -i \
+		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+		"${S}"/bin/cns_web
+
+	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
+
+	insinto /usr/share/cns
+	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
+	doins "${S}"/bin/cns_info
+
+	insinto /etc/profile.d
+	newins "${S}"/cns_solve_env cns_solve_env.csh
+	newins "${T}"/cns_solve_env_sh cns_solve_env.sh
+
+	dohtml \
+		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+		-f all_cns_info_template,omac,def \
+		-r doc/html/*
+}
+
+pkg_info() {
+		elog "Set OMP_NUM_THREADS to the number of threads you want."
+		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
+		elog "variable if using gcc (16384 should be good)."
+}
+
+pkg_postinst() {
+	pkg_info
+}
diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch
new file mode 100644
index 000000000000..45f5c318155f
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-gentoo.patch
@@ -0,0 +1,72 @@
+--- cns_solve_1.21/instlib/source/Makefile.proto	2000-09-07 20:35:33.000000000 +0200
++++ cns_solve_1.21/instlib/source/Makefile.proto.new	2009-07-14 09:18:37.000000000 +0200
+@@ -11,6 +11,8 @@
+ 
+ SHELL=/bin/sh
+ 
++cns_string=`date "+%y%m%d%H%M"`
++
+ # commands
+ RM = /bin/rm
+ 
+@@ -25,26 +27,20 @@
+ 
+ # rule for the fortran routines
+ $(OBJS): 
+-	@ echo "compiling: $(@:.o=.f)"; \
+-	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
++	$(F77) -c $(F77FLAGS) $(@:.o=.f)
+ 
+ # rule for the dynamic memory allocation C routines
+ dmemory.o: dmemory.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the machine specific C routines
+ machine_c.o: machine_c.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the executable itself
+ ../bin/cns_solve: $(DEPENDS) 
+-	@ echo ; echo "linking: cns_solve"; echo
+-	@ cns_string=`date "+%y%m%d%H%M"`; \
+-	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
+-	                                      $(LDFLAGS) \
+-	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
++	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
++	                                      $(CNS_FFTDIR) $(CNS_FFTLIB) $(OMPLIB); \
+ 	  if [ -x cns_solve-$$cns_string.exe ]; \
+ 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
+ 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
+@@ -59,7 +55,7 @@
+ 	@ echo; echo "flags:"; \
+ 	  echo " fortran -> [$(F77)] $(F77FLAGS)"; \
+ 	  echo "       c -> [$(CC)] $(CCFLAGS)"; \
+-	  echo "    link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB)"; \
++	  echo "    link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB)  $(OMP_LIB)"; \
+ 	  echo
+ 
+ # regenerate makefiles
+--- cns_solve_1.21/instlib/utils/Makefile	2004-08-30 00:40:35.000000000 +0200
++++ cns_solve_1.21/instlib/utils/Makefile.new	2009-07-14 09:50:27.000000000 +0200
+@@ -22,14 +22,14 @@
+ 	make clean
+ 
+ .f:
+-	$(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
++	$(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
+ 
+ .c:
+-	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
++	$(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
+ 
+ .l:
+ 	lex $(@).l
+-	$(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
++	$(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
+ 
+ relink:
+ 	@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`