From 40aaaa64e86ba6710bbeb31c4615a6ce80e75e11 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 28 Apr 2021 20:21:43 +0100 Subject: gentoo resync : 28.04.2021 --- sci-biology/glimmer/Manifest | 9 +-- .../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 ---------------------- .../glimmer/files/glimmer-3.02b-ldflags.patch | 20 +++-- sci-biology/glimmer/glimmer-3.02-r3.ebuild | 60 --------------- sci-biology/glimmer/glimmer-3.02b.ebuild | 26 +++---- 7 files changed, 26 insertions(+), 223 deletions(-) delete mode 100644 sci-biology/glimmer/files/glimmer-3.02-glibc210.patch delete mode 100644 sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch delete mode 100644 sci-biology/glimmer/files/glimmer-3.02-ldflags.patch delete mode 100644 sci-biology/glimmer/glimmer-3.02-r3.ebuild (limited to 'sci-biology/glimmer') 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) $(TGT) || exit 1/' src/c_make.gen || die - # GCC 4.3 include fix - sed -i 's/include /include /' src/Common/delcher.hh || die - epatch "${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 /include /' 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 -- cgit v1.2.3