gentoo resync : 28.04.2021

7 files changed, 26 insertions, 223 deletions

diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index 6455e2a011b1..ff6038c01462 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -1,11 +1,6 @@
-AUX glimmer-3.02-glibc210.patch 799 BLAKE2B e9c09d46982314f5780d5e958ec27f7b71955a1fa462f8c8086ed1ef36cd940742af897c0e0528101ec86d337ba30dfec3df463410748a3488b9a1f2b76c3f4a SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b
-AUX glimmer-3.02-jobserver-fix.patch 433 BLAKE2B c337abe08b47e9cdc3ea600e0ebea9b168ba0d6dfc087f1a3c1865583df148a126178acb9418fc330cda48152b5ee56e827efcaaa8b1c0d7c2810854c2738e2f SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d
-AUX glimmer-3.02-ldflags.patch 2057 BLAKE2B 1333aa5d94d218dfd7f986cdea3f7e5c4485e1ed3a3e0ff970b113b686035c3f3da3a3b7c2b747502ea772413f19cdbb15bc5988a26240eab7b380b7a8426ee1 SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8
 AUX glimmer-3.02b-jobserver-fix.patch 433 BLAKE2B c337abe08b47e9cdc3ea600e0ebea9b168ba0d6dfc087f1a3c1865583df148a126178acb9418fc330cda48152b5ee56e827efcaaa8b1c0d7c2810854c2738e2f SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d
-AUX glimmer-3.02b-ldflags.patch 2057 BLAKE2B 1333aa5d94d218dfd7f986cdea3f7e5c4485e1ed3a3e0ff970b113b686035c3f3da3a3b7c2b747502ea772413f19cdbb15bc5988a26240eab7b380b7a8426ee1 SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8
+AUX glimmer-3.02b-ldflags.patch 2091 BLAKE2B f4ff77a5b16896b349dfc7dd916b350b11afa61661216bea1292d772492eb94a911fcea6ae21fe13879fe0b91f1530ce757cce82c1a98a75569bb95fa6e97aa3 SHA512 4ffd4fdc5ec51c01e74e886814c61cb6d4268452d074168aca56ad36e2b5a15deda5305a7c45820ad00d6895ec9088062c932a28dda3c22f9d0a131f14e73c0a
 AUX glimmer-3.02b-rename_extract.patch 9286 BLAKE2B ce955f8f721f8043fe2beed82b7676e6503da20bd9a4cc556e1e29fcfcd9ffdfab1a430a98ece99f13a03241771f7b393d7c7290bf1d5c6652e67bdc5905950c SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342
-DIST glimmer302.tar.gz 5637075 BLAKE2B 07fc22a9192644c42291bd305a24bd7c40881cf5e8b668885ffdd5695100a2370b9cdbb275956e36df9007b1cb7bbfba84ab84863f26b70e68638fdf35e608d0 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c
 DIST glimmer302b.tar.gz 5637975 BLAKE2B 76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6
-EBUILD glimmer-3.02-r3.ebuild 1361 BLAKE2B e493ff1e9f6237b23f3d2a010385d955b1dcc1fc4668a16be7325711ed03d7444388b67a3e187bc7f18930dee933d770dc86eb3cd47dcf068a96e7f1170fd3a8 SHA512 0fd7e98d14981ea15c9b19d1a8a3af7ee316c9038d82956f232c9842ef476f2a5636ff87339dbcf1eb935448788fb3fd45caaefd90ce73d00c1bef05b17f0ad5
-EBUILD glimmer-3.02b.ebuild 1714 BLAKE2B d737bc73c36fd390c5b9235323f738a740c008571d37b87c74372a9ec7f1492bbbeb6a4c16b9a6cabee70a06ea76f2607406453307e98068e463cbde5656646b SHA512 df03f729fa5b0dd6b1e0121701e58d0c6a60b4e8d70d02bdebf6bd7ddd10523a7429c3e13ff4267e4835220cac3a15970565fbcac7979b400ff87707cbaca29c
+EBUILD glimmer-3.02b.ebuild 1676 BLAKE2B 3e81fee625fb53db07ddb9c782e0d6a73878592b276a51f741f7f46f15f0213cfccb2592a9e82b5735a4ef9a83a791d0a268de197cf9c1760d1b6f04b6bfbafe SHA512 880de5402658689993b818391a769b1f592febf98e5ba84be9fc9fc97c286287afbbae29133bb2e6c3badaac7874a0fca8f666be49f3a2e874cdf4c93c4fde05
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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 f6051ec82054..000000000000
--- 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 91498b116d12..000000000000
--- 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
-+	@+ $(dosubdirs)
- 
- 
- install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
deleted file mode 100644
index 0a04fbef1dcc..000000000000
--- a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-diff --git a/src/c_make.gen b/src/c_make.gen
-index 414dead..84c3030 100644
---- a/src/c_make.gen
-+++ b/src/c_make.gen
-@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(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/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
index 0a04fbef1dcc..dc41ef00de7e 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 = $(LOCAL_WORK)/obj
+ 
diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
deleted file mode 100644
index 9a32e3dbf895..000000000000
--- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-inherit eutils toolchain-funcs
-
-MY_PV=${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
-}
diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
index 4318b60ff949..c9332c5143a1 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