commit: d3ede632793d65970f45479128628a23355d175d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 5 13:30:33 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Apr 5 13:30:33 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d3ede632
sci-biology/glimmer: Remove old 3.02
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/glimmer/Manifest | 1 -
.../glimmer/files/glimmer-3.02-glibc210.patch | 24 ------
.../glimmer/files/glimmer-3.02-jobserver-fix.patch | 22 ------
.../glimmer/files/glimmer-3.02-ldflags.patch | 88 ----------------------
sci-biology/glimmer/glimmer-3.02-r3.ebuild | 60 ---------------
5 files changed, 195 deletions(-)
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index fc38be4881f..aa2a22056a4 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -1,2 +1 @@
-DIST glimmer302.tar.gz 5637075 BLAKE2B
07fc22a9192644c42291bd305a24bd7c40881cf5e8b668885ffdd5695100a2370b9cdbb275956e36df9007b1cb7bbfba84ab84863f26b70e68638fdf35e608d0
SHA512
c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c
DIST glimmer302b.tar.gz 5637975 BLAKE2B
76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11
SHA512
00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6
diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
deleted file mode 100644
index f6051ec8205..00000000000
--- a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
---- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056
+0000
-+++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000
-@@ -443,7 +443,7 @@
- // Return a subscript corresponding to character ch .
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (CONVERSION_STRING, tolower (ch));
- if (p == NULL)
-diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
---- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000
-+++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000
-@@ -1981,7 +1981,7 @@
- // model) for character ch .
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (ALPHA_STRING, tolower (Filter (ch)));
- if (p == NULL)
diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
deleted file mode 100644
index 91498b116d1..00000000000
--- a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
---- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100
-@@ -2,12 +2,12 @@
-
-
- all:
-- @ TGT=objs
-- @ $(dosubdirs)
-- @ TGT=libs
-- @ $(dosubdirs)
-- @ TGT=progs
-- @ $(dosubdirs)
-+ @+ TGT=objs
-+ @+ $(dosubdirs)
-+ @+ TGT=libs
-+ @+ $(dosubdirs)
-+ @+ TGT=progs
-+ @+ $(dosubdirs)
-
-
- install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
deleted file mode 100644
index 0a04fbef1dc..00000000000
--- a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-diff --git a/src/c_make.gen b/src/c_make.gen
-index 414dead..84c3030 100644
---- a/src/c_make.gen
-+++ b/src/c_make.gen
-@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
- #### Do not redefine if (a) passed in on command line, or (b)
- #### defined in an environment variable.
-
--ifneq "$(origin CC)" "environment"
--CC = cc
--endif
--
--ifneq "$(origin CPPFLAGS)" "environment"
--CPPFLAGS=
--endif
--
--ifneq "$(origin CFLAGS)" "environment"
--CFLAGS =
--endif
--
--ifneq "$(origin CDEFS)" "environment"
--CDEFS =
--endif
--
--ifneq "$(origin CXX)" "environment"
--CXX = g++
--endif
--
--ifneq "$(origin CXXFLAGS)" "environment"
--CXXFLAGS=
--endif
--
--ifneq "$(origin CXXDEFS)" "environment"
--CXXDEFS= -D__cplusplus
--endif
--
--ifneq "$(origin AR)" "environment"
--AR = ar
--endif
--
--ifneq "$(origin ARFLAGS)" "environment"
--ARFLAGS = rvs
--endif
--
--ifneq "$(origin LDFLAGS)" "environment"
--LDFLAGS =
--endif
-+CC ?= cc
-+CXX ?= g++
-+CXXFLAGS ?=
-+CXXDEFS = -D__cplusplus
-+AR ?= ar
-+ARFLAGS ?= rvs
-
- #### Delete default suffix rules
- .SUFFIXES:
-@@ -359,13 +326,13 @@ $(PROGS):
- cd $(LOCAL_OBJ); \
- if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
- $(LD_DIRS) $(filter-out lib%.a, $+) \
-- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
- else \
- cd $(LOCAL_OBJ); \
- if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
- $(LD_DIRS) $(filter-out lib%.a, $+) \
-- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- 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 $(LOCAL_WORK)/src/c_make.gen
-
- SUBDIRS = Common ICM Glimmer Util
-
--CFLAGS = -g -Wall
--CXXFLAGS = -g -Wall
--
--LDFLAGS = -g -lm
-+LIBS = -lm
-
-
- #AS_BUILD_DIR =$(LOCAL_WORK)
diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
deleted file mode 100644
index 9a32e3dbf89..00000000000
--- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-inherit eutils toolchain-funcs
-
-MY_PV=${PV//./}
-
-DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml";
-SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz";
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh"
-
-S="${WORKDIR}/${PN}${PV}"
-
-PATCHES=(
- "${FILESDIR}"/${P}-glibc210.patch
- "${FILESDIR}"/${P}-jobserver-fix.patch
- "${FILESDIR}"/${P}-ldflags.patch
- "${FILESDIR}"/${PN}-3.02b-rename_extract.patch
-)
-
-src_prepare() {
- sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
- -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die
"failed to rewrite paths"
- # Fix Makefile to die on failure
- sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen ||
die
- # GCC 4.3 include fix
- sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh
|| die
- epatch "${PATCHES[@]}"
-}
-
-src_compile() {
- emake \
- -C src \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- AR=$(tc-getAR) \
- CXXFLAGS="${CXXFLAGS}" \
- CFLAGS="${CFLAGS}" \
- LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
- rm bin/test || die
- dobin bin/*
-
- insinto /usr/share/${PN}
- doins -r scripts
-
- dodoc glim302notes.pdf
-}
