From f80543fa8ba49c8bb7f2d10e74cc0e53c7175336 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Tue, 18 Oct 2005 14:40:51 +0000 Subject: New version. Removing obsolete version. (Portage version: 2.0.51.22-r3) --- sci-chemistry/nmrpipe/ChangeLog | 9 +- sci-chemistry/nmrpipe/Manifest | 6 +- .../files/digest-nmrpipe-2.3.2005.167.14.44 | 10 ++ .../nmrpipe/files/digest-nmrpipe-20050616-r1 | 10 -- sci-chemistry/nmrpipe/files/env-nmrpipe | 23 ++++ sci-chemistry/nmrpipe/files/nmrpipe-20050616-env | 23 ---- .../nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild | 135 +++++++++++++++++++++ sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild | 129 -------------------- 8 files changed, 179 insertions(+), 166 deletions(-) create mode 100644 sci-chemistry/nmrpipe/files/digest-nmrpipe-2.3.2005.167.14.44 delete mode 100644 sci-chemistry/nmrpipe/files/digest-nmrpipe-20050616-r1 create mode 100644 sci-chemistry/nmrpipe/files/env-nmrpipe delete mode 100644 sci-chemistry/nmrpipe/files/nmrpipe-20050616-env create mode 100644 sci-chemistry/nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild delete mode 100644 sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog index 8b864276523a..5d3882460459 100644 --- a/sci-chemistry/nmrpipe/ChangeLog +++ b/sci-chemistry/nmrpipe/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/nmrpipe # Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/ChangeLog,v 1.4 2005/08/31 00:40:57 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/ChangeLog,v 1.5 2005/10/18 14:40:51 ribosome Exp $ + +*nmrpipe-2.3.2005.167.14.44 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette + -files/nmrpipe-20050616-env, +files/env-nmrpipe, + +nmrpipe-2.3.2005.167.14.44.ebuild, -nmrpipe-20050616-r1.ebuild: + New version. Removing obsolete version. *nmrpipe-20050616-r1 (31 Aug 2005) diff --git a/sci-chemistry/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest index 1cb7bab3927e..dabbae20624d 100644 --- a/sci-chemistry/nmrpipe/Manifest +++ b/sci-chemistry/nmrpipe/Manifest @@ -1,5 +1,5 @@ -MD5 a795e5521920ba8f4a9a2ea4c0e5e15d nmrpipe-20050616-r1.ebuild 4217 +MD5 1f32699892c9647adeab23c603336aa6 nmrpipe-2.3.2005.167.14.44.ebuild 4621 MD5 ed6fbd16c2ce349850d79d010ddd5da9 ChangeLog 1162 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254 -MD5 2e7903ea90b6ace1bfa67c6efb6e875d files/digest-nmrpipe-20050616-r1 585 -MD5 29c1ecf7eda6ce5cb66a3cc7eafc00f1 files/nmrpipe-20050616-env 499 +MD5 1e3746832adf60875e61757b9ffdd1ef files/digest-nmrpipe-2.3.2005.167.14.44 584 +MD5 29c1ecf7eda6ce5cb66a3cc7eafc00f1 files/env-nmrpipe 499 diff --git a/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.3.2005.167.14.44 b/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.3.2005.167.14.44 new file mode 100644 index 000000000000..474073efefa7 --- /dev/null +++ b/sci-chemistry/nmrpipe/files/digest-nmrpipe-2.3.2005.167.14.44 @@ -0,0 +1,10 @@ +MD5 619771c84baeffe7e786ddd07c0d73ba nmrpipe.linux9.tar.Z 22505078 +MD5 bd7b0dfd903eab1df014bb9d7356612b xview_fonts.tar.Z 2183991 +MD5 06d27f018d0abd3e2e35fcd923423af3 xview.linux9.tar.Z 4047400 +MD5 0a03f5c8fb0fa48deb803b00ac5f4a3f dyn.tar.Z 37506563 +MD5 2fa433021210fe75c275910b67693015 mfr.tar.Z 829580 +MD5 b33e195e36e9c35a970632dc9670d312 pdbH.tar.Z 75004655 +MD5 af1c0e23c9d78025b9173fcbbb1c1f07 valpha.tar 490800640 +MD5 f8df76a619d702153a19b23f1678aca6 acme.tar.Z 11681951 +MD5 72a4802dcc912569d645f4cb5b27f5e5 binval.com 3209 +MD5 8c128c3c6a0840fd20f54ae40b330224 install.com 20812 diff --git a/sci-chemistry/nmrpipe/files/digest-nmrpipe-20050616-r1 b/sci-chemistry/nmrpipe/files/digest-nmrpipe-20050616-r1 deleted file mode 100644 index 252530dd10f2..000000000000 --- a/sci-chemistry/nmrpipe/files/digest-nmrpipe-20050616-r1 +++ /dev/null @@ -1,10 +0,0 @@ -MD5 b17803971db1c1a5949cc33d50190275 nmrpipe.linux9.tar.Z 21918245 -MD5 bd7b0dfd903eab1df014bb9d7356612b xview_fonts.tar.Z 2183991 -MD5 06d27f018d0abd3e2e35fcd923423af3 xview.linux9.tar.Z 4047400 -MD5 70ae354d8ee365a9998a6679b9e88085 dyn.tar.Z 37503947 -MD5 185f4d4090d95181443d7fe4321489ae mfr.tar.Z 1066703 -MD5 b33e195e36e9c35a970632dc9670d312 pdbH.tar.Z 75004655 -MD5 af1c0e23c9d78025b9173fcbbb1c1f07 valpha.tar 490800640 -MD5 f8df76a619d702153a19b23f1678aca6 acme.tar.Z 11681951 -MD5 72a4802dcc912569d645f4cb5b27f5e5 binval.com 3209 -MD5 08d2b3dec7d37cf0685bdf4240512301 install.com 20519 diff --git a/sci-chemistry/nmrpipe/files/env-nmrpipe b/sci-chemistry/nmrpipe/files/env-nmrpipe new file mode 100644 index 000000000000..beb9d707eb4f --- /dev/null +++ b/sci-chemistry/nmrpipe/files/env-nmrpipe @@ -0,0 +1,23 @@ +# Platform +BINTYPE="linux9" + +# NMRPipe +NMRBASE="/opt/nmrpipe" +NMRTXT="${NMRBASE}/nmrtxt" +MANPATH="${NMRBASE}/man" +PATH="${NMRBASE}/bin" +# Auxiliary NMRPipe scripts +# PATH="${PATH}:${NMRBASE}/com" + +# Dynamo +DYNAMO_DIR="${NMRBASE}/dynamo" +DYNAMO_PARAMS="${DYNAMO_DIR}/params" +SURF_DIR="${DYNAMO_DIR}/surface" +PATH="${PATH}:${DYNAMO_DIR}/tcl" +DYNAMO_KEY="2002084" + +# PDBH +PDBH_BASE="${NMRBASE}/pdb" +PDBH_DIR="${PDBH_BASE}/pdbH" +PDBH_LIST="${PDBH_BASE}/pdbH.list" +PDBH_TAB="${PDBH_BASE}/resolution.tab" diff --git a/sci-chemistry/nmrpipe/files/nmrpipe-20050616-env b/sci-chemistry/nmrpipe/files/nmrpipe-20050616-env deleted file mode 100644 index beb9d707eb4f..000000000000 --- a/sci-chemistry/nmrpipe/files/nmrpipe-20050616-env +++ /dev/null @@ -1,23 +0,0 @@ -# Platform -BINTYPE="linux9" - -# NMRPipe -NMRBASE="/opt/nmrpipe" -NMRTXT="${NMRBASE}/nmrtxt" -MANPATH="${NMRBASE}/man" -PATH="${NMRBASE}/bin" -# Auxiliary NMRPipe scripts -# PATH="${PATH}:${NMRBASE}/com" - -# Dynamo -DYNAMO_DIR="${NMRBASE}/dynamo" -DYNAMO_PARAMS="${DYNAMO_DIR}/params" -SURF_DIR="${DYNAMO_DIR}/surface" -PATH="${PATH}:${DYNAMO_DIR}/tcl" -DYNAMO_KEY="2002084" - -# PDBH -PDBH_BASE="${NMRBASE}/pdb" -PDBH_DIR="${PDBH_BASE}/pdbH" -PDBH_LIST="${PDBH_BASE}/pdbH.list" -PDBH_TAB="${PDBH_BASE}/resolution.tab" diff --git a/sci-chemistry/nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild b/sci-chemistry/nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild new file mode 100644 index 000000000000..a2e9c9ada4a3 --- /dev/null +++ b/sci-chemistry/nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild @@ -0,0 +1,135 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/nmrpipe-2.3.2005.167.14.44.ebuild,v 1.1 2005/10/18 14:40:51 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="${PN}.linux9.tar.Z + xview_fonts.tar.Z + xview.linux9.tar.Z + dyn.tar.Z + mfr.tar.Z + pdbH.tar.Z + valpha.tar + acme.tar.Z + binval.com + install.com" + +SLOT="0" +IUSE="" +# Right now, precompiled executables are only available for Linux on the +# x86 architecture. The maintainer chose to keep the sources closed, but +# says he will gladly provide precompiled executables for other platforms +# if there are such requests. +KEYWORDS="-* ~x86" + +# The maintainer absolutely wants to control redistribution. +RESTRICT="fetch" + +DEPEND="app-shells/tcsh + dev-lang/f2c" + +RDEPEND="${DEPEND} + dev-lang/tcl + dev-lang/tk + dev-tcltk/blt + media-gfx/gnuplot + sci-chemistry/rasmol + sys-libs/libtermcap-compat + virtual/x11 + x11-libs/xview" + +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 ${PN}.linux9.tar.Z xview_fonts.tar.Z xview.linux9.tar.Z \ + dyn.tar.Z mfr.tar.Z pdbH.tar.Z valpha.tar acme.tar.Z; do + ln -s "${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 ${i} || die "Failed to remove archive symlinks." + done + # Remove some of the bundled applications and libraries; they are + # provided by Gentoo instead. + rm -r xview XView nmrbin.linux9/{0.0,lib,*timestamp,xv,gnuplot*,rasmol*} \ + || die "Failed to remove unnecessary libraries." + # Remove the initialisation script generated during the installation. + # It contains incorrect hardcoded paths; only the "nmrInit.com" script + # should be used. + rm com/nmrInit.linux9.com || die "Failed to remove broken init script." + # Make the precompiled Linux binaries executable. + chmod +x nmrbin.linux9/* || die "Failed to make programs executable." + # Set the correct path to NMRPipe in the auxiliary scripts. + cd com + for i in *; do + sed -e "s%/u/delaglio%${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 +} diff --git a/sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild b/sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild deleted file mode 100644 index a3d346ca4e0d..000000000000 --- a/sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild +++ /dev/null @@ -1,129 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrpipe/nmrpipe-20050616-r1.ebuild,v 1.1 2005/08/31 00:40:57 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="${PN}.linux9.tar.Z - xview_fonts.tar.Z - xview.linux9.tar.Z - dyn.tar.Z - mfr.tar.Z - pdbH.tar.Z - valpha.tar - acme.tar.Z - binval.com - install.com" -# The maintainer absolutely wants to control redistribution. -RESTRICT="fetch" - -SLOT="0" -IUSE="" -# Right now, precompiled executables are only available for Linux on the -# x86 architecture. The maintainer chose to keep the sources closed, but -# says he will gladly provide precompiled executables for other platforms -# if there are such requests. -KEYWORDS="-* ~x86" - -RDEPEND="virtual/x11 - dev-lang/f2c - dev-lang/tcl - dev-lang/tk - dev-tcltk/blt - media-gfx/gnuplot - app-shells/tcsh - sys-libs/libtermcap-compat - x11-libs/xview - sci-chemistry/rasmol" - -S="${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 ${PN}.linux9.tar.Z xview_fonts.tar.Z xview.linux9.tar.Z \ - dyn.tar.Z mfr.tar.Z pdbH.tar.Z valpha.tar acme.tar.Z; do - ln -s "${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 ${i} - done - # Remove some of the bundled applications and libraries; they are - # provided by Gentoo instead. - rm -r xview XView nmrbin.linux9/{0.0,lib,*timestamp,xv,gnuplot*,rasmol*} - # Remove the initialisation script generated during the installation. - # It contains incorrect hardcoded paths; only the "nmrInit.com" script - # should be used. - rm com/nmrInit.linux9.com - # Make the precompiled Linux binaries executable. - chmod +x nmrbin.linux9/* - # Set the correct path to NMRPipe in the auxiliary scripts. - cd com - for i in *; do - sed -e "s%/u/delaglio%${NMRBASE}%" -i ${i} || die - done - # Remove installation log files. - cd "${S}" - rm *.log -} - -src_install() { - newenvd "${FILESDIR}"/${P}-env 40${PN} - insinto /opt/${PN} - insopts -m0755 - doins -r * - dosym /opt/${PN}/nmrbin.linux9 /opt/${PN}/bin -} - -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/opt/${PN}/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 -} -- cgit v1.2.3-65-gdbad