sci-biology/libgtextutils: Initial addition

Closes: https://bugs.gentoo.org/486380
Package-Manager: Portage-2.3.19, Repoman-2.3.6

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>