[gentoo-commits] proj/sci:master commit in: sci-biology/seqclean/, profiles/, sci-biology/seqclean/files/

[Andrew Ammerlaan]

commit:     8f7b92289adb3326f0e6cb43697fdbcc4a8a950a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:20:38 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:20:38 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f7b9228

sci-biology/seqclean: remove last-rited pack

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask                              |   1 -
 .../seqclean/files/seqclean-110625-build.patch     | 135 ---------------------
 sci-biology/seqclean/metadata.xml                  |  12 --
 sci-biology/seqclean/seqclean-110625.ebuild        |  54 ---------
 4 files changed, 202 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index f8e1e4d32..6b58c272e 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -37,7 +37,6 @@
 # Bug #798015, removal in 30 days.
 # Perhaps these packages work with the newer ncbi-tools++? If anyone is actively
 # using these packages please open a bug report
-sci-biology/seqclean
 sci-chemistry/talosn
 # revdep of seqclean
 sci-biology/rum

diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch
deleted file mode 100644
index b5797618f..000000000
--- a/sci-biology/seqclean/files/seqclean-110625-build.patch
+++ /dev/null
@@ -1,135 +0,0 @@
- mdust/Makefile    |   18 +++++++++---------
- mdust/fastafile.c |    3 ++-
- mdust/mdust.c     |    1 +
- trimpoly/Makefile |   16 ++++++++--------
- 4 files changed, 20 insertions(+), 18 deletions(-)
-
-diff --git a/mdust/Makefile b/mdust/Makefile
-index 81bf4e9..0c75e69 100644
---- a/mdust/Makefile
-+++ b/mdust/Makefile
-@@ -1,40 +1,40 @@
- # Useful directories
- 
- # Directories to search for header files
--SEARCHDIRS := -I. -I- 
-+SEARCHDIRS := -I. -iquote
- 
- 
- #SYSTYPE :=     $(shell uname)
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    =
- LOADLIBES := 
- 
- .PHONY : all
- all:    mdust
- 
- mdust:  ./mdust.o ./dust.o ./fastafile.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 
-diff --git a/mdust/fastafile.c b/mdust/fastafile.c
-index 6c14b99..5f70f14 100644
---- a/mdust/fastafile.c
-+++ b/mdust/fastafile.c
-@@ -1,7 +1,8 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <malloc.h>
--
-+#include <string.h>
-+#include <stdlib.h>
- #include "fastafile.h"
- 
- 
-diff --git a/mdust/mdust.c b/mdust/mdust.c
-index f2bae99..c3ee686 100644
---- a/mdust/mdust.c
-+++ b/mdust/mdust.c
-@@ -1,6 +1,7 @@
- #include <stdlib.h>
- #include <stdio.h>
- #include <ctype.h>
-+#include <string.h>
- #include "dust.h"
- #include "fastafile.h"
- 
-diff --git a/trimpoly/Makefile b/trimpoly/Makefile
-index 84db22d..71145c2 100644
---- a/trimpoly/Makefile
-+++ b/trimpoly/Makefile
-@@ -3,28 +3,28 @@
- # Directories to search for header files
- SEARCHDIRS := -I.
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    = 
- LOADLIBES =
- SYSTYPE :=     $(shell uname)
- #ifeq ($(SYSTYPE), Linux)
-@@ -37,7 +37,7 @@ SYSTYPE :=     $(shell uname)
- all:    trimpoly
- 
- trimpoly:  ./trimpoly.o color_c.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 

diff --git a/sci-biology/seqclean/metadata.xml b/sci-biology/seqclean/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/seqclean/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>

diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
deleted file mode 100644
index f98fdf3b8..000000000
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences"
-HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
-for i in seqcl_scripts mdust trimpoly; do
-	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz"
-done
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-lang/perl
-	sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-build.patch
-)
-
-src_prepare() {
-	default
-	# disable the necessity to install Mailer.pm with this tool
-	einfo "Disabling mailer feature within seqclean"
-	sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die
-	tc-export CC CXX
-}
-
-src_compile() {
-	for i in mdust trimpoly; do
-		LDLFAGS="${LDFLAGS}" \
-			emake -C "${S}"/${i}
-	done
-}
-
-src_install() {
-	dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx}
-	newdoc seqclean/README README.seqclean
-	for i in mdust trimpoly; do
-		dobin ${i}/${i}
-	done
-
-	einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own"
-	einfo "fasta file with vector sequences you want to remove from sequencing"
-	einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"
-}