reinit the tree, so we can have metadata

7 files changed, 209 insertions, 0 deletions

diff --git a/sci-chemistry/cyana/Manifest b/sci-chemistry/cyana/Manifest
new file mode 100644
index 000000000000..1cf1996ce476
--- /dev/null
+++ b/sci-chemistry/cyana/Manifest
@@ -0,0 +1,9 @@
+AUX 2.1-exec.patch 1959 SHA256 fe8835c6dcdb6a8befa32e6bff1b761c5c6ae6131f73750e18724fb96f9a9623 SHA512 43f04008b623e95e09cc323abd504c4f5bf708bde4771f2e334ae5d4ca59c24cfcaf34a3ad7c5b65ebb4587614343982fe377a226648098e02de8bdaa1c36a1d WHIRLPOOL 5ff8eedecd3e680e0f17917b6bd3c08bca6a0412f4e3e1693163af431eae3e9534d9fd87e574feaa11268988770a6f15ef5b3e070995995200f91521b8f1302a
+AUX 2.1-expire.patch 578 SHA256 723d69026e63995b281ae36582f5114562a1c4d6295d311ca2eb2900a1dc7b95 SHA512 7816f284a7af23c5d87a5a464ea36e7a1b09e73516852b85fac0d71bb8376639788f3f9395f8a6fd9365906d2aaadbd060f2194c7af3b68a24927adefcd56c40 WHIRLPOOL 8443238b88c5869225b6d68841a44fcdd618df21df9b07998b35897ad907a0b4e4264ad5925a46d944cfc7996f2ff9618380ac4f14f1b1f55926595eecedcbc2
+AUX 2.1-typo.patch 484 SHA256 ef05c4254cf859e804c44cdfa5774aca5a2f1aa853f0b6c0bccee837db2a5b8b SHA512 298e5053e4261477a11f0dff2339f198e50e92a96b98c5aea82e3a432b806b1ea0baa3638ef6e65dee315be3223510a804e2c849a82fdda0a1cf296de9d89db4 WHIRLPOOL 18b1db0e746630a9c040bd80b9f6cddff1ceaec2e92ce6d5583f6fb830d565012d25cfba284eb194f7b7930c5b01338b302b8dd7be01d56d62a580ac546ad572
+AUX 2.1-xiar.patch 385 SHA256 c8d4daddaafa1388b87c7b107206df873fe98dc418db36ab48bfb2c60b3435e6 SHA512 ce4c27b70d0c432b33f76b4ff76d004f525243269064f1af439bf42ab9783edd9dc19712b277d8e08bb692a28c40db7007040da1635cbd3c432029e4fe6c680f WHIRLPOOL 76d7e103437a7b76a0411fe563e082f90de514d67cf20e0ef0e7e2f9754230ac65a175471ec0685a8a3be9fa2d612a38137f4d03f10014a6e6dd547b4ff37100
+DIST cyana-2.1.tar.gz 2203650 SHA256 4b49d23eda3a327074fa337c7ee13262e93fb2b92cc6feb9139dfb7695bdeded SHA512 20f5369e47198000927ee9a60beda34d265fddcd6be59f0d5d81ac23691b7e870ca674bdd7215a13bc849586411a007ebb1ff46072b55f255a6d796359067be8 WHIRLPOOL dfc60a456c166d98bbdb60227a2dae63d12ea9fb7375dede3d372a6dbf0785bfd0c8b1069d985a6ee775ab136405b553ff9336a2603d139d81d853f0681f5167
+EBUILD cyana-2.1.ebuild 1439 SHA256 f00f45b10735aa60a57b90aa05980382b5b9c8e04569bc5a559a02d4eb0c47af SHA512 47108af1f37d2adb2fd111da3db51f60feedc4d4f7c4da5327b3217626e8d6826b45993e900ca43d252c98d42216e6a878ada5039be7385bd18d2dac67c3891f WHIRLPOOL 57d9b19272cbba10998769f070ee9d0364bd4854575372b7d51a74b9289d42a1659e9b07aea3e02e7e24d02156d2654eafe24e22924b41b5d72f2de72df3ef00
+MISC ChangeLog 2658 SHA256 3ec8746a7c30c9b68e8d8028a52b68404a5335ab7f64c52e4cb24c4a433a6b7d SHA512 08491938901922cea8a9bcc35337eede0a58e21b6ac8dee287b87ae3d080744bba0055afeaac7b1a81b882b2b7a0ef36126109d344b7c13d45b7341c14c50f0a WHIRLPOOL 1b557630f90673b70317bb103e08a86a79855fbd97e99c2fc39c3b57f133e9c06df2aa551afb768e3e4fc7f2803775e20c0180ce99b358da174ca7be63d09716
+MISC ChangeLog-2015 2576 SHA256 9c77e2e9956b062cfab2b1a0d91d4652ff85189fb4f2273676fefe279497e80e SHA512 8c9fa3acaaa16f33d4d2700c1ebeced86f2ec7c3affe27449d92f909fa7a27f23072fa333d9029d74e10bbf9d6e3d3961b2b92b73094be425b3080cfc55c1059 WHIRLPOOL 5beb86e4ad958efc8ba808adf4b4bf1a5062f13acfbc474363a17c3a916f7348e23e420b90d2dd98bd9e17ee543f8233e78e94bc408ff3b16aadb5a043515bf0
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/cyana/cyana-2.1.ebuild b/sci-chemistry/cyana/cyana-2.1.ebuild
new file mode 100644
index 000000000000..f017c9af247c
--- /dev/null
+++ b/sci-chemistry/cyana/cyana-2.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="Combined assignment and dynamics algorithm for NMR applications"
+HOMEPAGE="http://www.las.jp/english/products/cyana.html"
+SRC_URI="${P}.tar.gz"
+
+LICENSE="CYANA"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RESTRICT="fetch"
+
+# we need libg2c for gfortran # 136988
+DEPEND="dev-lang/ifc"
+RDEPEND="${DEPEND}"
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "http://www.las.jp/english/products/cyana.html"
+	elog "and get a copy of ${A}."
+	elog "Place it in ${DISTDIR}."
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-typo.patch \
+		"${FILESDIR}"/${PV}-exec.patch \
+		"${FILESDIR}"/${PV}-expire.patch \
+		"${FILESDIR}"/${PV}-xiar.patch
+
+	cat >> etc/config <<- EOF
+	VERSION=${PV}
+	SHELL=${EPREFIX}/bin/sh
+	FC=ifort
+	FFLAGS=${FFLAGS} -openmp -threads
+	FFLAGS2=${FFLAGS} -openmp -threads
+	CC=$(tc-getCC)
+	AR=xiar
+	RANLIB=ranlib
+	FORK=g77fork.o
+	LDFLAGS=${LDFLAGS} -reentrancy threaded -openmp
+	LIBS=
+	DEFS=-Dintel
+	SYSTEM=intel
+	EOF
+}
+
+src_compile() {
+	cd src || die
+	emake
+}
+
+src_install() {
+	dobin cyana{job,table,filter,clean}
+	newbin src/${PN}/${PN}exe.* ${PN}
+	insinto /usr/share/${PN}
+	doins -r lib macro help
+	use examples && doins -r demo
+
+	cat >> "${T}"/20cyana <<- EOF
+	CYANALIB="${EPREFIX}/usr/share/${PN}"
+	EOF
+
+	doenvd "${T}"/20cyana
+}
diff --git a/sci-chemistry/cyana/files/2.1-exec.patch b/sci-chemistry/cyana/files/2.1-exec.patch
new file mode 100644
index 000000000000..28cd88d3eee6
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-exec.patch
@@ -0,0 +1,77 @@
+diff --git a/cyana b/cyana
+index 4f746cf..a7ff060 100755
+--- a/cyana
++++ b/cyana
+@@ -45,16 +45,13 @@ shift `expr $optind - 1`
+ 
+ if [ "$h" ]; then usage=1; fi
+ if [ "$usage" ]; then
+-  echo "Usage: $prog -hctx parameters ..."					         
++  echo "Usage: $prog -hS parameters ..."					         
+   echo  									         
+   echo "       -h	     help"						         
+   echo "       -c command    command to start program (must contain \$exefile)"          
+   echo "       -S            run in safe mode, i.e. within one directory"				         
+-  echo "       -t system     explicit system type"				         
+-  echo "       -x	     display name of executable without executing it"	         
+   exit 2
+ fi
+-if [ "$c" ]; then cmd="$c"; fi
+ sys=$t
+ mode=$x
+ safe=$S
+@@ -65,23 +62,6 @@ safe=$S
+ eval ${PROG}ARG='$*'
+ export ${PROG}ARG
+ 
+-
+-# ------ Set library name ------ 
+-
+-f=$0
+-if [ `echo $f | sed 's,^/.*,+,'` != "+" ]; then f=`which $0`; fi
+-odir=`pwd`
+-while [ "`ls -l $f | awk '{ print substr($1,1,1) }'`" = "l" ]; do
+-  l=`ls -l $f | awk '{ i = NF; print $i }'`
+-  cd `dirname $f`; cd `dirname $l`; l=`pwd`/`basename $l`
+-  f=$l
+-done
+-cd `dirname $f`
+-libdir=`pwd | sed 's,/src/'${prog}'$,,'`
+-cd $odir
+-eval ${PROG}LIB=$libdir
+-export ${PROG}LIB
+-
+ if [ "$safe" ]; then 
+   CYANAINIT=initsafe; export CYANAINIT
+ fi
+@@ -89,29 +69,4 @@ fi
+ 
+ # ------ Start the program ------
+ 
+-if [ -d $libdir/src/$prog ]; then
+-  exe=$libdir/src/$prog/$exe
+-else
+-  exe=$libdir/$exe
+-fi
+-if [ "$sys" = "" ]; then
+-  sys=`$libdir/etc/identify`
+-  files="$exe.$sys* $exe.gnu $exe.*"
+-else
+-  files=$exe.$sys
+-fi
+-for exefile in $files; do
+-  if [ -x $exefile ]; then
+-    if [ "$mode" ]; then
+-      echo $exefile; exit 0
+-    else
+-      if [ "`echo $cmd | grep -c '\$exefile'`" -gt 0 ]; then
+-        eval exec $cmd
+-      else
+-        eval exec $cmd $exefile
+-      fi
+-    fi
+-  fi
+-done
+-echo "No executable found in \"`dirname $exe`\"."
+-exit 1
++exec cyana
diff --git a/sci-chemistry/cyana/files/2.1-expire.patch b/sci-chemistry/cyana/files/2.1-expire.patch
new file mode 100644
index 000000000000..e18008286f68
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-expire.patch
@@ -0,0 +1,15 @@
+--- src/inclan/unix.for.orig	2011-01-05 14:56:46.572193759 +0100
++++ src/inclan/unix.for	2011-01-05 14:57:27.833627375 +0100
+@@ -206,11 +206,8 @@
+       end if
+       if (iwbeg.lt.0) then
+         iwbeg=igttim
+-        iexpir=(julday(12,31,2010)-julday(1,1,1970))*24*3600
+-        if (iwbeg.gt.iexpir) call fatmsg ('License expired.')
++        iexpir=iwbeg+100
+         j=(iexpir-iwbeg)/(24*3600)
+-        if (j.lt.1000)
+-     *    call wrnmsg ('License expires in '//plural(j,'day')//'.')
+       end if
+       iwall=igttim-iwbeg
+ c      print *,'iwall = ',iwall,iwbeg,idat,itim
\ No newline at end of file
diff --git a/sci-chemistry/cyana/files/2.1-typo.patch b/sci-chemistry/cyana/files/2.1-typo.patch
new file mode 100644
index 000000000000..3f011a9b2c28
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-typo.patch
@@ -0,0 +1,13 @@
+diff --git a/src/cyana/putpro.f b/src/cyana/putpro.f
+index d4080f9..4490225 100644
+--- a/src/cyana/putpro.f
++++ b/src/cyana/putpro.f
+@@ -66,7 +66,7 @@ c     ------------------------------------------------------ BMRB header
+      *    '   _Mol_residue_sequence',
+      *    ';'
+         do i=1,nr,20
+-          write (iunit,'(20A1))') (rcode(rnam(j)),j=i,min(nr,i+19))
++          write (iunit,'(20A1)') (rcode(rnam(j)),j=i,min(nr,i+19))
+         end do
+ 
+         write (iunit,'(A)')
diff --git a/sci-chemistry/cyana/files/2.1-xiar.patch b/sci-chemistry/cyana/files/2.1-xiar.patch
new file mode 100644
index 000000000000..e8393253d7f6
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-xiar.patch
@@ -0,0 +1,16 @@
+ src/inclan/Makefile |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/inclan/Makefile b/src/inclan/Makefile
+index fc5a8bf..482d48f 100644
+--- a/src/inclan/Makefile
++++ b/src/inclan/Makefile
+@@ -35,7 +35,7 @@ clean:
+ 
+ inclan.a: $(OBJS)
+ 	rm -f $@
+-	ar rc $@ $(OBJS)
++	$(AR) rc $@ $(OBJS)
+ 	if [ "$(RANLIB)" ]; then $(RANLIB) $@; fi
+ 
+ inclan.o: inclan.for
diff --git a/sci-chemistry/cyana/metadata.xml b/sci-chemistry/cyana/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-chemistry/cyana/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+</pkgmetadata>