AUX 1.2.1-aria.patch 15006 RMD160 b358747845e8d53f450e654f493dedbe400f537f SHA1 234dde547748ba95eb7b94ffac7bfcc9bfd22991 SHA256 08585a1e88b8b8da0f983e934a2859b128e4cba5e714af3b6ed40f334fdbe982
AUX 1.2.1-aria2.3.patch 658 RMD160 a372156b7a783cb78c81aadae2eca5c64c9630e5 SHA1 b3cb35d793d7aa01c2c14ea7848a29b81a735bdd SHA256 c393799beabda5f61a7dcad9aaa4d211c14eb17b1ffd5200c3306c7ef71d19f3
AUX 1.2.1-gentoo.patch 2411 RMD160 a82893524541961a9797fd2bb84982e609fda717 SHA1 7d3168a9cf7622923138022a5683aa65b5d5c34d SHA256 58972606d23d87fdeb08c9e37d9d5c536983e5a1ad4647dedd5b283ef67bc52c
+AUX 1.2.1-ifort.patch 5346 RMD160 106cf7dc7b4e13674fdf34ca0fd9af78effbc84b SHA1 26ccc71740ee2539352009f730b79b2ae20b5047 SHA256 bac35147159fac06fcb3a03a4f09c56224d4ee852b86a771121d98c42f3a9c65
AUX 1.2.1-parallel.patch 641 RMD160 dffcaf7a4d7c79b9362640b64e677a7fde04ac80 SHA1 5de790cee7acf9ff4a87a61fdc866c330ef6d6f1 SHA256 7cd3312c35d2dbbd2146fdfa977f9866365c4a7be16787b1ba5d9807ff823d31
AUX cns_solve_env_sh 7070 RMD160 4104b22476a61a80c7adae8a363da1dd4ab4f136 SHA1 30ba978f4862fd94d9fa939cbb7c3eb55ece46cd SHA256 da571cba2a2244e571870b1783fd6cdce1b595e14234cfb43011e9e9eb50151c
DIST aria2.2.tar.gz 1710084 RMD160 b96a900befd5521649ccce84d4d5b93d30709799 SHA1 faa5ff9e7682026afc334f1c8b3b10259a5e69f9 SHA256 a1695ee11b06a045c4b4bb9f0113d1e48c86e12d4149c0dcb505ca894069d054
EBUILD cns-1.2.1-r1.ebuild 5531 RMD160 93f382ecb94f6b6a21108182a2aae18547bc704a SHA1 f80f7203f79cd527b2ccdd2755971a21a6b87cba SHA256 0866f9e38ce28d128db71974d1832f7fc6124f0d11b02f90111cd8a5434b075c
EBUILD cns-1.2.1-r2.ebuild 6085 RMD160 bbf32a77b2c3d84becb95d390704b77943348ac1 SHA1 4e09e5ce780edb8f78eea2456be1aebd0ebef3a9 SHA256 26812e41de70704d1327b5e9abcdd73eb63b03162aa0ff3e340594d1da0506ec
EBUILD cns-1.2.1-r3.ebuild 6212 RMD160 c42de027f4b43219617f1ff14ee7f2183719ba38 SHA1 d4c2c9155047d1da4225af0f9f8d391ed02b53f9 SHA256 9bb0e75981db8f7feff60465311b4840b398c1f8a095dfe0ebc9a3888d59addc
+EBUILD cns-1.2.1-r4.ebuild 6536 RMD160 2d6ffd2f5d33cb1ee82f1941a845f2880b7196f1 SHA1 862abc4c0324cda2bff4a1624b8172517f7e833e SHA256 c7c92a842e450e203f1098b05edd9a82545c331b008b4b7ece8a63539685774f
EBUILD cns-1.2.1.ebuild 5574 RMD160 23000fd54ce250a3dbf40ab71d12c539fda0d9fd SHA1 42c852c40d23eeec1280359d5adfe8c51a7ebf24 SHA256 7c1f6871416f516773af3cd23d8be9c2b0e978401898d5932622a2dd2b121301
EBUILD cns-1.2.ebuild 3497 RMD160 9e097171ebd44f1a7e5dd317beeb6b65aefac2f6 SHA1 3afc4b415d2ef559b717843a05bc6afb8ee651a2 SHA256 1a6094c8bca3797e62c375a2370cc7425e9c1dd1106d20f202681bc5a87da1fc
-MISC ChangeLog 4009 RMD160 128a7099f4c412edfaad7262854e15673d40c83e SHA1 68560988c3e219ea3861064468ca5526471918d1 SHA256 3d0805ba87e9381040bd1c1c6dcea16fafb1a7b67764f863b2ae35c74e05be4a
+MISC ChangeLog 4152 RMD160 3cb037666c2b579e81527d08e8917d72fce107ec SHA1 03d46a719f4af3051e22e004ee9044975d41ad76 SHA256 470bf8329e75d21ddd59f7ea31f3b037f00da24ce6a76bc7ae0d358b888b636f
MISC metadata.xml 302 RMD160 d60d9cd875115eaba68ad4b504bff76b39a136b0 SHA1 ecdd8feeea2de489927403f1941acfc582c17222 SHA256 a374144760a8ac1f72b1c625c41f98cee3f74511c964133bda119da580664c50
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--- /dev/null
+# Copyright 1999-2010 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-r4.ebuild,v 1.1 2010/04/05 21:15:30 jlec Exp $
+
+EAPI="3"
+
+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="${MY_P}_all-mp.tar.gz
+ aria? ( aria2.3.1.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh
+ !app-text/dos2unix"
+DEPEND="${RDEPEND}"
+PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )"
+
+RESTRICT="fetch"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="gfortran ifc"
+
+pkg_nofetch() {
+ elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
+ use aria && elog "and http://aria.pasteur.fr/"
+ 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
+ epatch "${FILESDIR}"/${PV}-parallel.patch
+
+ if use aria; then
+ pushd "${WORKDIR}"/aria* >& /dev/null
+ # Update the cns sources in aria for version 1.2.1
+ epatch "${FILESDIR}"/1.2.1-aria2.3.patch
+
+ # Update the code with aria specific things
+ cp -rf cns/src/* "${S}"/source/
+ popd >& /dev/null
+ fi
+
+ # the code uses Intel-compiler-specific directives
+ if [[ ${FORTRANC} == gfortran ]]; then
+ epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
+ use openmp && \
+ OMPLIB="-lgomp" && append-flags -fopenmp
+ COMP="gfortran"
+ use amd64 && \
+ append-fflags -fdefault-integer-8
+ else
+ epatch "${FILESDIR}"/${PV}-ifort.patch
+ use openmp && OMPLIB="-lgomp" && \
+ append-flags -openmp && append-ldflags -openmp
+ COMP="ifort"
+ use amd64 && append-fflags -i8
+ append-fflags -Vaxlib
+ append-ldflags -Vaxlib
+ fi
+
+ use amd64 && \
+ append-cflags "-DINTEGER='long long int'"
+
+ # Set up location for the build directory
+ # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+ cp "${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" \
+ "${T}"/cns_solve_env_sh
+
+ einfo "Fixing shebangs..."
+ find "${S}" -type f \
+ -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
+}
+
+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
+ # -j1 doesn't mean we do no respect MAKEOPTS!
+ emake -j1 \
+ 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="${OMPLIB}" \
+ compiler="${COMP}" \
+ install \
+ || 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 ${EPREFIX}/usr:g" \
+ -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns: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=${EPREFIX}/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}"/*linux*/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 "${S}"/*linux*/utils/Makefile
+
+ dobin "${S}"/*linux*/utils/* || die "install utils failed"
+
+ sed -i \
+ -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+ "${S}"/bin/cns_web || die
+
+ dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
+
+ insinto /usr/share/cns
+ doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
+ doins "${S}"/bin/cns_info || die
+
+ insinto /etc/profile.d
+ newins "${S}"/cns_solve_env cns_solve_env.csh || die
+ newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
+
+ 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/* || die
+}
+
+pkg_info() {
+ if use openmp; then
+ 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)."
+ fi
+}
+
+pkg_postinst() {
+ pkg_info
+}
--- /dev/null
+diff --git a/source/angledb.f b/source/angledb.f
+index 28ad657..eaa847d 100644
+--- a/source/angledb.f
++++ b/source/angledb.f
+@@ -1416,10 +1416,10 @@ C include files
+ C local variables
+ INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS
+ INTEGER THETYPE, CURPSIS, CURPHIS
+- INTEGER CLASSINDEX
++ INTEGER CLASINDEX
+ DOUBLE PRECISION K1, CUTOFF
+ CHARACTER*4 THENAME
+- CHARACTER*20 CLASSNAME
++ CHARACTER*20 CLASNAME
+ C begin
+ C
+ IF (ANGLEDBFLAG) THEN
+@@ -1450,10 +1450,10 @@ C
+ ELSE IF (WD(1:4).EQ.'CLAS') THEN
+ OLDCLASS = CURANGLEDBCLASS
+ CALL NEXTWD('class name =')
+- CLASSNAME = WD(1:20)
++ CLASNAME = WD(1:20)
+ ANGLEDBMODE = NEW
+ DO COUNT = 1, NANGLEDBCLASSES
+- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN
++ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN
+ ANGLEDBMODE = UPDATE
+ CURANGLEDBCLASS = COUNT
+ END IF
+@@ -1472,7 +1472,7 @@ C
+ END IF
+ NANGLEDBCLASSES = NANGLEDBCLASSES + 1
+ CURANGLEDBCLASS = NANGLEDBCLASSES
+- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME
++ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME
+ ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS
+ END IF
+ C
+@@ -1733,16 +1733,16 @@ C
+ & HEAP(ANGLEDBTPTR))
+ ELSE IF (WD(1:4).EQ.'CLAS') THEN
+ CALL NEXTWD('Class name>')
+- CLASSNAME = WD(1:20)
+- CLASSINDEX = 0
++ CLASNAME = WD(1:20)
++ CLASINDEX = 0
+ DO COUNT = 1, NANGLEDBCLASSES
+ IF (ANGDBCLASSNAMES(COUNT).EQ.
+- & CLASSNAME) THEN
++ & CLASNAME) THEN
+ PRINTTHISCLASS(COUNT) = .TRUE.
+- CLASSINDEX = COUNT
++ CLASINDEX = COUNT
+ END IF
+ END DO
+- IF (CLASSINDEX.EQ.0) THEN
++ IF (CLASINDEX.EQ.0) THEN
+ CALL DSPERR('ANGLEDB',
+ & 'unknown class. Using first.')
+ PRINTTHISCLASS(1) = .TRUE.
+diff --git a/source/rama.f b/source/rama.f
+index c5d14f2..3063e7b 100644
+--- a/source/rama.f
++++ b/source/rama.f
+@@ -1468,11 +1468,11 @@ C include files
+ C local variables
+ INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS,
+ & THETYPE, CURPSIS, CURPHIS,
+- & CURCHIS, CURTHTS, CLASSINDEX
++ & CURCHIS, CURTHTS, CLASINDEX
+ INTEGER CLEN
+ DOUBLE PRECISION K1, CUTOFF
+ CHARACTER*4 THENAME
+- CHARACTER*50 CLASSNAME
++ CHARACTER*50 CLASNAME
+ C begin
+ C
+ C this is used by READRAMA2 to hold the selection
+@@ -1503,10 +1503,10 @@ C
+ ELSE IF (WD(1:4).EQ.'CLAS') THEN
+ OLDCLASS = CURRAMACLASS
+ CALL NEXTWD('class name =')
+- CLASSNAME = WD(1:50)
++ CLASNAME = WD(1:50)
+ RAMAMODE = NEW
+ DO COUNT = 1, NRAMACLASSES
+- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN
++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN
+ RAMAMODE = UPDATE
+ CURRAMACLASS = COUNT
+ END IF
+@@ -1525,7 +1525,7 @@ C
+ END IF
+ NRAMACLASSES = NRAMACLASSES + 1
+ CURRAMACLASS = NRAMACLASSES
+- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME
++ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME
+ END IF
+ C
+ C set force constant for current class,
+@@ -1954,18 +1954,18 @@ C
+ & HEAP(RAMAATOMPTR), 0)
+ ELSE IF (WD(1:4).EQ.'CLAS') THEN
+ CALL NEXTWD('Class name>')
+- CLASSINDEX = 0
++ CLASINDEX = 0
+ DO COUNT = 1, NRAMACLASSES
+- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME)
+- & CLASSINDEX = COUNT
++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME)
++ & CLASINDEX = COUNT
+ END DO
+- IF (CLASSINDEX.EQ.0) THEN
++ IF (CLASINDEX.EQ.0) THEN
+ CALL DSPERR('RAMA',
+ & 'unknown class. Using first.')
+- CLASSINDEX = 1
++ CLASINDEX = 1
+ END IF
+ CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR),
+- & HEAP(RAMAATOMPTR), CLASSINDEX)
++ & HEAP(RAMAATOMPTR), CLASINDEX)
+ ELSE
+ CALL DSPERR('RAMA',
+ & 'Expected ALL or CLASs.')
projects / gentoo.git / commitdiff