commit: 48960a50011d74f396e30fa4e11b0774fc6c33cb Author: NHOrus <jy6x2b32pie9 <AT> yahoo <DOT> com> AuthorDate: Mon Feb 17 18:41:12 2025 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Wed Feb 19 18:04:09 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=48960a50
sci-chemistry/molmol: Consolidate patches, remove seds, pin C to gnu17 This uses C polymorphism with function pointers without signature. Fixing that without major re-engineering would be problematic. Five sed expressions are consolidated into patch, re-engineeded when needed, eg. for CC and MCFLAGS. Where possible, patches are moved from eapply inside src_prepare to PATCHES variable, order of preparations is changed for better understanding. Closes: https://bugs.gentoo.org/944200 Signed-off-by: NHOrus <jy6x2b32pie9 <AT> yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/40620 Signed-off-by: Sam James <sam <AT> gentoo.org> .../files/molmol-2k_p2-transform-makefiles.patch | 40 ++++++++ sci-chemistry/molmol/molmol-2k_p2-r10.ebuild | 103 +++++++++++++++++++++ 2 files changed, 143 insertions(+) diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch new file mode 100644 index 000000000000..6129ed03b3ab --- /dev/null +++ b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch @@ -0,0 +1,40 @@ +Transformed multiple seds to this patch. `MOLMOLHOME` is the runtime variable +that depends on knowledge of paths that I didn't think of how to correctly +pass beyond editing it with sed. For everything else, it is here and changed +to work correctly with build system. +Rolled up sed transformations were to made build system non-parallel, +fix environmental variables, remove sleep and add use right shell and +build dependencies in startup script. +--- a/makedef.lnx ++++ b/makedef.lnx +@@ -11,12 +11,12 @@ + + XINCL = -I/usr/X11R6/include + +-CC=gcc ++CC ?= gcc + MCPPFLAGS = +-MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686 ++MCFLAGS := $(CFLAGS) + + RANLIB = /bin/true +-WAIT = sleep 2 ++WAIT = sleep 0 + SHELL = /bin/sh + CPP = /lib/cpp + +--- a/molmol ++++ b/molmol +@@ -1,9 +1,10 @@ +-#!/bin/ksh ++#!/bin/sh + # + # startup script for MOLMOL + # + +-MOLMOLHOME=/opt/group/MOLMOL ++MOLMOLHOME=/; ++MOLMOLDEV="Motif/OpenGL" + export MOLMOLHOME + export MOLMOLDEV + diff --git a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild new file mode 100644 index 000000000000..f9425f749a99 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild @@ -0,0 +1,103 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit desktop toolchain-funcs flag-o-matic + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" + +# Original page dead +#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"; +HOMEPAGE=" + http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html + http://pjf.net/science/molmol.html +" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2 + https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png +" +S="${WORKDIR}" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + || ( + ( + media-libs/mesa[X(+)] + x11-libs/libGLw + ) + media-libs/mesa[motif(-),X(+)] + ) + media-libs/libjpeg-turbo:= + media-libs/libpng:= + media-libs/tiff:= + sys-libs/zlib + virtual/glu + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo + media-fonts/font-adobe-100dpi +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-gcc14-fix.patch + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff + "${WORKDIR}"/patches/ldflags.patch + "${WORKDIR}"/patches/opengl.patch + "${WORKDIR}"/patches/cast.patch + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + "${WORKDIR}"/patches/${P}-fink.patch + "${WORKDIR}"/patches/wild.patch + + "${FILESDIR}"/${P}-transform-makefiles.patch +) + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + default + eapply -p0 "${WORKDIR}"/patches/libpng15.patch + rm -rf tiff* + + sed \ + -e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR}|" \ + -i "${S}"/molmol || die + + ln -s makedef.lnx "${S}"/makedef || die + + # Parallel build fails (#880621) and cannot be disabled by MAKEOPTS + # (#880621, #941488). + find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die + + # https://bugs.gentoo.org/944200 + # uses C polymorphism. Can't be trivially patched + append-cflags -std=gnu17 + tc-export AR CC +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + doexe src/main/molmol + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + make_desktop_entry "${PN}" MOLMOL + newicon "${DISTDIR}/${PN}_256.png" "${PN}.png" + + einstalldocs + dodoc HISTORY +}
