commit: 08a072e6e7aeb962594f489db2000ea89c2599bb Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Apr 5 13:30:36 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Apr 5 13:30:36 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08a072e6
sci-biology/glimmer: Port to EAPI 7 Closes: https://bugs.gentoo.org/731892 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap <AT> gentoo.org> .../glimmer/files/glimmer-3.02b-ldflags.patch | 20 ++++++++++------- sci-biology/glimmer/glimmer-3.02b.ebuild | 26 ++++++++++------------ 2 files changed, 24 insertions(+), 22 deletions(-) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch index 0a04fbef1dc..dc41ef00de7 100644 --- a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -1,8 +1,6 @@ -diff --git a/src/c_make.gen b/src/c_make.gen -index 414dead..84c3030 100644 --- a/src/c_make.gen +++ b/src/c_make.gen -@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc +@@ -200,45 +200,11 @@ #### Do not redefine if (a) passed in on command line, or (b) #### defined in an environment variable. @@ -48,13 +46,12 @@ index 414dead..84c3030 100644 +CC ?= cc +CXX ?= g++ +CXXFLAGS ?= -+CXXDEFS = -D__cplusplus +AR ?= ar +ARFLAGS ?= rvs #### Delete default suffix rules .SUFFIXES: -@@ -359,13 +326,13 @@ $(PROGS): +@@ -359,13 +325,13 @@ cd $(LOCAL_OBJ); \ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ $(LD_DIRS) $(filter-out lib%.a, $+) \ @@ -70,11 +67,9 @@ index 414dead..84c3030 100644 true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ fi ; -diff --git a/src/c_make.glm b/src/c_make.glm -index 0decc17..b82131c 100644 --- a/src/c_make.glm +++ b/src/c_make.glm -@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen +@@ -8,18 +8,14 @@ SUBDIRS = Common ICM Glimmer Util @@ -86,3 +81,12 @@ index 0decc17..b82131c 100644 #AS_BUILD_DIR =$(LOCAL_WORK) + INC_IMPORT_DIRS += \ + $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) \ + $(LOCAL_WORK)/inc +-LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib /usr/lib /usr/shlib /usr/X11R6/lib \ +- $(SYBASE)/lib ++LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib + + OBJ_SEARCH_PATH = $(LOCAL_WORK)/obj + diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild index 4318b60ff94..c9332c5143a 100644 --- a/sci-biology/glimmer/glimmer-3.02b.ebuild +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -1,28 +1,25 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI="5" +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"; SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"; +S="${WORKDIR}/${PN}3.02" LICENSE="Artistic" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="app-shells/tcsh +RDEPEND=" + app-shells/tcsh sci-biology/elph" -#S="${WORKDIR}/${PN}${PV}" -S="${WORKDIR}/${PN}3.02" - PATCHES=( "${FILESDIR}"/${P}-jobserver-fix.patch "${FILESDIR}"/${P}-ldflags.patch @@ -37,12 +34,13 @@ src_prepare() { # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die # - sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die - sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die - sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die + sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die + sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die sed -i "s/@ if/if/" src/c_make.gen || die + # avoid file collision on /usr/bin/extract #247394 - epatch "${PATCHES[@]}" + default } src_compile() { @@ -60,7 +58,7 @@ src_install() { rm bin/test || die dobin bin/* - insinto /usr/share/${PN} + insinto /usr/share/glimmer doins -r scripts dodoc glim302notes.pdf
