diff options
Diffstat (limited to 'sci-biology')
5 files changed, 132 insertions, 0 deletions
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest new file mode 100644 index 000000000000..9480b9ec6419 --- /dev/null +++ b/sci-biology/libgtextutils/Manifest @@ -0,0 +1 @@ +DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6 diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch new file mode 100644 index 000000000000..f7f608b792d2 --- /dev/null +++ b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch @@ -0,0 +1,61 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -15,7 +15,7 @@ + + AC_CONFIG_AUX_DIR(config) + AC_CONFIG_MACRO_DIR([m4]) +-AM_CONFIG_HEADER(config.h) ++AC_CONFIG_HEADERS([config.h]) + AM_INIT_AUTOMAKE([dist-bzip2]) + + # dynamic library version +@@ -25,12 +25,12 @@ + + AC_PROG_CC + AC_PROG_CXX +-AC_PROG_LIBTOOL ++LT_INIT + + dnl --enable-wall +-EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror" ++EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal" + AC_ARG_ENABLE(wall, +-[ --enable-wall Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)], ++[ --enable-wall Enable many common GCC warnings (-Wall,-Wextra etc., default enabled)], + [case "${enableval}" in + yes) wall=true ;; + no) wall=false ;; +@@ -42,22 +42,6 @@ + CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}" + fi + +-dnl --enable-debug +-AC_ARG_ENABLE(debug, +-[ --enable-debug Enable debug mode (default enabled)], +-[case "${enableval}" in +- yes) debug=true ;; +- no) debug=false ;; +- *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;; +-esac],[debug=true]) +-if test "$debug" = "true" +-then +- CFLAGS="${CFLAGS} -DDEBUG -g -O1" +- CXXFLAGS="${CFLAGS} -DDEBUG -g -O1" +-else +- CFLAGS="${CFLAGS} -O3" +- CXXFLAGS="${CFLAGS} -O3" +-fi + + + dnl --enable-tuple-parser-check +--- a/Makefile.am ++++ b/Makefile.am +@@ -9,7 +9,7 @@ + # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + + EXTRA_DIST = reconf configure +-SUBDIRS = m4 src doc tests ++SUBDIRS = src doc tests + + pkgconfigdir = $(libdir)/pkgconfig + pkgconfig_DATA = gtextutils.pc diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch new file mode 100644 index 000000000000..490b4be9b91b --- /dev/null +++ b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch @@ -0,0 +1,22 @@ +From d8bb66d26288293ebde7f8d88979c13c208ffce5 Mon Sep 17 00:00:00 2001 +From: Assaf Gordon <assafgordon@gmail.com> +Date: Mon, 14 Aug 2017 11:52:09 -0600 +Subject: [PATCH] text_line_reader: adjust to new compilers + +Fixes https://github.com/agordon/libgtextutils/issues/10 . +--- + src/gtextutils/text_line_reader.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/gtextutils/text_line_reader.cpp b/src/gtextutils/text_line_reader.cpp +index fede933..f0984d5 100644 +--- a/src/gtextutils/text_line_reader.cpp ++++ b/src/gtextutils/text_line_reader.cpp +@@ -44,6 +44,6 @@ bool TextLineReader::next_line() + if (input_stream.eof()) + return false; + +- return input_stream ; ++ return input_stream.good() ; + } + diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild new file mode 100644 index 000000000000..8f0455e5322c --- /dev/null +++ b/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Gordon Text utils Library" +HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit/" +SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/${P}.tar.bz2" + +LICENSE="AGPL-3" +SLOT="0/0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +PATCHES=( + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-gcc6.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf --disable-static +} + +src_install() { + default + + # package installs .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml new file mode 100644 index 000000000000..138cb7705c0a --- /dev/null +++ b/sci-biology/libgtextutils/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |