New upstream version (fixes bug #151627). Removed old version.

(Portage version: 2.1.1)

3 files changed, 164 insertions, 2 deletions

diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog
index 48ff1b6606c8..ecb342815441 100644
--- a/sci-chemistry/nmrpipe/ChangeLog
+++ b/sci-chemistry/nmrpipe/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/nmrpipe
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/ChangeLog,v 1.9 2006/09/20 05:09:00 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/ChangeLog,v 1.10 2006/10/18 00:10:58 ribosome Exp $
+
+*nmrpipe-2.5.2006.184.15.37 (18 Oct 2006)
+
+  18 Oct 2006; Olivier Fisette <ribosome@gentoo.org>
+  -nmrpipe-2.3.2005.167.14.44.ebuild, +nmrpipe-2.5.2006.184.15.37.ebuild:
+  New upstream version (fixes bug #151627, thanks to Stephen Floor
+  <snf@extrospective.net> for reporting.) Removing old version to avoid digest
+  mismatches.
 
   20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
   (#148281) Change herd to sci-chemistry from sci.
@@ -50,4 +58,3 @@
   24 May 2005; Olivier Fisette <ribosome@gentoo.org>
   +files/nmrpipe-20050415-env, +metadata.xml, +nmrpipe-20050415.ebuild:
   Initial import.
-
diff --git a/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.5.2006.184.15.37 b/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.5.2006.184.15.37
new file mode 100644
index 000000000000..cd4f23e9fb0c
--- /dev/null
+++ b/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.5.2006.184.15.37
@@ -0,0 +1,24 @@
+MD5 f8df76a619d702153a19b23f1678aca6 acme.tar.Z 11681951
+RMD160 fdcf35fab1b63ddda55288b1b2ed0f82c8299bef acme.tar.Z 11681951
+SHA256 5713452a1461e636f0de48e5ce3476fc0ae60b3f78a0288744f45e455f3445d9 acme.tar.Z 11681951
+MD5 451f23435825423f872f4c93adedac84 binval.com 3210
+RMD160 9cfa8c837aad976c97b689b745950cb2aa020938 binval.com 3210
+SHA256 f0d541a727e98618b3ffc1c6045c43a689d1b133869046cce40fecab2f00edfa binval.com 3210
+MD5 9f3deb8bf11d4a5e7f25c81028bba027 dyn.tar.Z 37424311
+RMD160 b5004d623a0be7c89fbc97347df85b421c27626d dyn.tar.Z 37424311
+SHA256 87f068d6c67c5c94fd39bb0561bfb1b5f77e5e1c24409edc934d7f083403b4b8 dyn.tar.Z 37424311
+MD5 bea8ad55530dbdbf4852584f5ae51186 install.com 21431
+RMD160 9b8ac9106577408e5637f3f0fa32cad6fdf0cf2a install.com 21431
+SHA256 24bdba38392b29ca2c3601e83dc70b563377017dd591e2f50256c1442ed11c94 install.com 21431
+MD5 a964a997d3f858fce09f06d2d049c214 mfr.tar.Z 899961
+RMD160 0c6f4ca5b63a894291b5185872fdecf96b5980f0 mfr.tar.Z 899961
+SHA256 90efc5c7ba219aee54259a730709a925ad7be6c52cf75a7944a8ab0b3bda5001 mfr.tar.Z 899961
+MD5 45d1c2502ab0497d5d1dda8e42f75046 nmrpipe.linux9.tar.Z 22155253
+RMD160 689047923b0199f480cf03cee0cb9bb3cb65655f nmrpipe.linux9.tar.Z 22155253
+SHA256 5e8accb37ec00b1ead2f718c26978101c82ece394cc08a72687fa836cfc4b544 nmrpipe.linux9.tar.Z 22155253
+MD5 b33e195e36e9c35a970632dc9670d312 pdbH.tar.Z 75004655
+RMD160 c0152166dfda441a8a1519eaca4bcdf998ae0cfb pdbH.tar.Z 75004655
+SHA256 b00458696d3b90de76c382f449d18a6b6affca6cb51dd66434c9848dc8a920d5 pdbH.tar.Z 75004655
+MD5 af1c0e23c9d78025b9173fcbbb1c1f07 valpha.tar 490800640
+RMD160 da5779f72680ccc8b88bde8c485db26665970423 valpha.tar 490800640
+SHA256 6072ac73245404d5810bef9300d76328585fcfb4bce9d517815624bcc0a9634c valpha.tar 490800640
diff --git a/sci-chemistry/nmrpipe/nmrpipe-2.5.2006.184.15.37.ebuild b/sci-chemistry/nmrpipe/nmrpipe-2.5.2006.184.15.37.ebuild
new file mode 100644
index 000000000000..eee731bbad99
--- /dev/null
+++ b/sci-chemistry/nmrpipe/nmrpipe-2.5.2006.184.15.37.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/nmrpipe-2.5.2006.184.15.37.ebuild,v 1.1 2006/10/18 00:10:58 ribosome Exp $
+
+DESCRIPTION="Spectral visualisation, analysis and Fourier processing"
+# The specific terms of this license are printed automatically on startup
+# by some NMRPipe applications. The user also has to accept them before
+# downloading the package.
+LICENSE="as-is"
+HOMEPAGE="http://spin.niddk.nih.gov/bax/software/NMRPipe/"
+# The NMRPipe installation script which we are not allowed to modify
+# requires all the following to be present for a complete installation.
+# Many of the bundled applications and libraries are afterwards deleted
+# (by this ebuild). The Gentoo provided applications and libraries are
+# used instead. The notable exception is the Tcl/Tk libraries; NMRPipe
+# requires a modified version of these. Unfortunately, this requires to
+# redefine the location of the libraries, which is done by sourcing an
+# initialisation script. NMRPipe users are used to this, and this ebuild
+# also prints a notice to this effect.
+SRC_URI="${PN}.linux9.tar.Z
+	dyn.tar.Z
+	mfr.tar.Z
+	pdbH.tar.Z
+	valpha.tar
+	acme.tar.Z
+	binval.com
+	install.com"
+
+SLOT="0"
+IUSE=""
+# Right now, precompiled executables are only available for Linux on the
+# x86 architecture. The maintainer chose to keep the sources closed, but
+# says he will gladly provide precompiled executables for other platforms
+# if there are such requests.
+KEYWORDS="-* ~x86"
+
+# The maintainer absolutely wants to control redistribution.
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh"
+
+RDEPEND="${DEPEND}
+	dev-lang/tcl
+	dev-lang/tk
+	dev-tcltk/blt
+	sys-libs/libtermcap-compat
+	sys-libs/ncurses
+	x11-libs/xview
+	|| ( x11-libs/libX11 virtual/x11 )"
+
+S="${WORKDIR}"
+NMRBASE="/opt/${PN}"
+
+pkg_nofetch() {
+	einfo "Please visit:"
+	einfo "\t${HOMEPAGE}"
+	einfo
+	einfo "Contact the package maintainer, then download the following files:"
+	for i in ${A}; do
+		einfo "\t${i}"
+	done
+	einfo
+	einfo "Place the downloaded files in your distfiles directory:"
+	einfo "\t${DISTDIR}"
+	echo
+}
+
+src_unpack() {
+	# The installation script will unpack the package. We just provide symlinks
+	# to the archive files, ...
+	for i in ${PN}.linux9.tar.Z dyn.tar.Z mfr.tar.Z \
+			pdbH.tar.Z valpha.tar acme.tar.Z; do
+		ln -s "${DISTDIR}"/${i} ${i}
+	done
+	# ... copy the installation scripts ...
+	cp "${DISTDIR}"/{binval.com,install.com} .
+	# ... and make the installation scripts executable.
+	chmod +x binval.com install.com
+}
+
+src_compile() {
+	# Unset DISPLAY to avoid the interactive graphical test.
+	DISPLAY="" ./install.com "${S}" || die
+	# Remove the symlinks for the archives and the installation scripts.
+	for i in ${A}; do
+		rm ${i} || die "Failed to remove archive symlinks."
+	done
+	# Remove some of the bundled applications and libraries; they are
+	# provided by Gentoo instead.
+	rm -r nmrbin.linux9/{0.0,lib,*timestamp,xv,gnuplot*,rasmol*} \
+		|| die "Failed to remove unnecessary libraries."
+	# Remove the initialisation script generated during the installation.
+	# It contains incorrect hardcoded paths; only the "nmrInit.com" script
+	# should be used.
+	rm com/nmrInit.linux9.com || die "Failed to remove broken init script."
+	# Make the precompiled Linux binaries executable.
+	chmod +x nmrbin.linux9/* || die "Failed to make programs executable."
+	# Set the correct path to NMRPipe in the auxiliary scripts.
+	cd com
+	for i in *; do
+		sed -e "s%/u/delaglio%${NMRBASE}%" -i ${i} || die \
+			"Failed patching scripts."
+	done
+	# Remove installation log files.
+	cd "${S}"
+	rm *.log || die "Failed to remove installation log."
+}
+
+src_install() {
+	newenvd "${FILESDIR}"/env-${PN} 40${PN} || die "Failed to install env file."
+	insinto ${NMRBASE}
+	insopts -m0755
+	doins -r * || die "Failed to install application."
+	dosym ${NMRBASE}/nmrbin.linux9 ${NMRBASE}/bin || die \
+		"Failed to symlink binaries."
+}
+
+pkg_postinst() {
+	echo
+	ewarn "Before using NMRPipe applications, users must source the following"
+	ewarn "csh script, which will set the necessary environment variables:"
+	ewarn "\t${NMRBASE}/com/nmrInit.com"
+	ewarn
+	ewarn "Be aware that this script redefines the locations of the Tcl"
+	ewarn "libraries. This could break other non-NMRPipe Tcl applications"
+	ewarn "run in the same session."
+	ewarn
+	ewarn "Using Dynamo does not require running an additional initialisation"
+	ewarn "script. The necessary environment variables should already be set."
+	echo
+}