sci-chemistry/massxpert: Drop old; punt base.eclass

Package-Manager: portage-2.2.8/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

8 files changed, 191 insertions, 118 deletions

diff --git a/sci-chemistry/massxpert/ChangeLog b/sci-chemistry/massxpert/ChangeLog
index b1ee9c857c34..b4399613c078 100644
--- a/sci-chemistry/massxpert/ChangeLog
+++ b/sci-chemistry/massxpert/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/massxpert
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/ChangeLog,v 1.13 2013/06/19 04:10:42 bicatali Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/ChangeLog,v 1.14 2014/01/06 15:24:25 jlec Exp $
+
+*massxpert-3.4.0 (06 Jan 2014)
+
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> -massxpert-1.7.6.ebuild,
+  massxpert-2.0.5.ebuild, +massxpert-3.4.0.ebuild,
+  -files/massxpert-1.7.6-gcc43.patch, +files/massxpert-3.4.0-gentoo.patch,
+  metadata.xml:
+  Drop old; punt base.eclass
 
   19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml:
   Changed herd to sci-chemistry
diff --git a/sci-chemistry/massxpert/Manifest b/sci-chemistry/massxpert/Manifest
index 6baff305e2d2..00b2f69ee452 100644
--- a/sci-chemistry/massxpert/Manifest
+++ b/sci-chemistry/massxpert/Manifest
@@ -1,18 +1,28 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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 AUX massxpert-2.0.5-gentoo.patch 2751 SHA256 10e3a50334915c15f932948f35fac195e7231423ac8f5914ad6037b78f0924ce SHA512 0037a7fa5993806a5786dfe5342658108a55354a42ef6d391a915c8ee2d02d5c373fbb5d0ba92bb24a3962a69f23f902656f685e998da42ba8c56aa845b9b33d WHIRLPOOL 21d70f2a9659b607b486593a06a15fea7073b47a599d7bdf2d213c72ce9b23abebe594f755643aabdc87fee457cc138f29cb48fa38b8a3c38903ffcc4583698f
-DIST massxpert-1.7.6.tar.gz 19676075 SHA256 d6a939981d19772b2c6e2b9e2b2df69817ef8f60e706bd94cb6e2b5f67740eef
-DIST massxpert-2.0.5.tar.gz 13603475 SHA256 11f7f1599a587be923ed0b58e753e1f9296e0c3c0acfb5e3980579e768600e5c
-EBUILD massxpert-1.7.6.ebuild 1401 SHA256 556da07c0e1c64a0cfa5dabf10d3103fb26896baf248c90e30ad123900bc39b3 SHA512 90aa0d3859a2bdb0f52990f41eefb0d7f583be89d291c873779cef69ffad9eb227a11afcb0c09c3079f134877fa07abe75028bcc080581de94389253fb62edd0 WHIRLPOOL 53dbc24dde9caede6d6f06f5ffff23db9721665a4997110d520bd8856eb8a0c79dcbbe89046d8bfdb7ce9381726c5e702d5e9e8fd0f7b552f68bddc3227510ef
-EBUILD massxpert-2.0.5.ebuild 1359 SHA256 c6a2d86ca5cf071b6f41266a909c8db4e7e2b672d448a8c1288471bf6a20b1f7 SHA512 6243ec9169229ddfd1b275e7e1542c2b00e70ee121a1585e093cf5f0e1e010de2dcbc01f76e4f82029bdd1fc913345792ce807061645dcab51c482b0c9ed93a4 WHIRLPOOL 87f299d29c5211932f2fc38de8fb0a7d4fedd4955128e561a2384f5b7e5b109f484721d0edc1c3fe92228723ee6a00024ada21baa08958e59d771f35c6ca8c62
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+AUX massxpert-3.4.0-gentoo.patch 2990 SHA256 f70439cd7a35b0582fa0adf862e858124dd0481ae00f455a953fa32a8b9f2aca SHA512 a3901821c803e28ff28f507ccf0509e58184c1ce02fcc76ebf4e36af4130ccee0cbe94212802b8caa03cfad2d09d926ed805b57eaf49ddc49e9045eeba0e6d25 WHIRLPOOL 615d0de16100b7d5324ef9123009c609bc60e8780457de24c919614de4dbef15a9bcba980e70980872306dc9c5d07be95bc423f6b2ce4cd6a6d277d605386622
+DIST massxpert-2.0.5.tar.gz 13603475 SHA256 11f7f1599a587be923ed0b58e753e1f9296e0c3c0acfb5e3980579e768600e5c SHA512 49c1d8fa4324907d04c79dddad66eecae34ba1dded98594838b4cbb88ad022abe3f8fbd7f2aeee73baafc17a03397b1776f2e6fdabf4e2ac4e4f6d6eeb86ca2f WHIRLPOOL dba641144835d303eaf181a70aabee11dc14a43c8fe508ad33eb2ffe3c1c8a11eaa1ae066a8e9134e9d6c891cea5fc2dba503ca5e53acf62eb8b532d52c1bf3e
+DIST massxpert-3.4.0.tar.bz2 16544044 SHA256 b06314722b4cbdf68dc76e55933a79487848c655fc65341a8dbc707ed89cc9e8 SHA512 50e8eaab145ab7fa225725b113d6840168b88db7d2ee194b176bc88eabf4f44c20f8dc0680986d659de1f94f2e0c6ae10d54e17e2d8b3b5aa6a9a9bf57a508de WHIRLPOOL 4578801c2dd4eee7390eadb299f3d55af29d0a48365f96ba6d6488a07792e47882e191f8eda05b6b261d9a972bf7f92f160d4a5fbbcc216ed7ffda32fcfee6ed
+EBUILD massxpert-2.0.5.ebuild 1318 SHA256 03e44940953c2363c9af31a0c868383c6c3503190a2575bba004533309a5fc1e SHA512 486f3f275cb4543354e2491193e85797c89bd72aa95a738d7d322976e7bd9dfa77bbf9ec809c0c736a529e840a2c78ba13c889f2824bc55d351b5093b8484321 WHIRLPOOL 686183635d03445c2864df075b89fa5b38870902034820b48cd8250fe96df636857fd91bfec1110a070a90a6d348d31687f1bc7248a57e1baff46f89ab2f479e
+EBUILD massxpert-3.4.0.ebuild 1260 SHA256 e7319c5bf77f6fe8ad364efbac7ab6752b465488c1bb9c76ee1755c2544d0587 SHA512 ee8e09ae2cb791046141cc93946ea1c1fb7e68f708542c698d56f14af40e50a7a1de7de004165c12adbecd0fc5d64ad3a74df2ec897b7058a36eb6c59790dcc9 WHIRLPOOL 4c7cecb23851d520d9a470a16dd6640ec2c868befdebb5d69bb9513fcd786f65c5899fdeb95f8e6eec7b48de11cd9b8aa1c0f1414f74e6ba88951088efc36f72
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diff --git a/sci-chemistry/massxpert/files/massxpert-1.7.6-gcc43.patch b/sci-chemistry/massxpert/files/massxpert-1.7.6-gcc43.patch
deleted file mode 100644
index 44a46e202adb..000000000000
--- a/sci-chemistry/massxpert/files/massxpert-1.7.6-gcc43.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- lib/userSpec.cpp.orig	2008-07-15 22:01:23.000000000 +0200
-+++ lib/userSpec.cpp	2008-07-15 22:02:22.000000000 +0200
-@@ -41,7 +41,8 @@
- 
- 
- /////////////////////// Std includes
--//#include <stdlib.h>
-+#include <cstdlib>
-+
- 
- 
- /////////////////////// Local includes
-
-
---- gui/isotopicPatternCalculationDlg.cpp.orig	2008-07-15 22:09:07.000000000 +0200
-+++ gui/isotopicPatternCalculationDlg.cpp	2008-07-15 22:09:56.000000000 +0200
-@@ -61,8 +61,10 @@
- 
- 
- /////////////////////// Std includes
--#include <math.h>
-+#include <cmath>
- #include <algorithm>
-+#include <limits>
-+
- 
- 
- /////////////////////// Local includes
diff --git a/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch
new file mode 100644
index 000000000000..fc0fc4f606cf
--- /dev/null
+++ b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch
@@ -0,0 +1,91 @@
+ CMakeLists.txt                   | 20 ++++----------------
+ gui/configurationSettingsDlg.cpp | 10 ++++------
+ 2 files changed, 8 insertions(+), 22 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index fec954b..b87d157 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -24,10 +24,10 @@ SET (CMAKE_VERBOSE_MAKEFILE ON)
+ #############################################################
+ # Enable warnings and treat them as errors, on GNU/Linux only
+ IF (UNIX)
+-  SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall -Werror.")
++  SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall.")
+   
+   IF (PEDANTIC)
+-    ADD_DEFINITIONS (-Wall -Werror)
++    ADD_DEFINITIONS (-Wall)
+   ENDIF (PEDANTIC)
+ ENDIF (UNIX)
+ 
+@@ -64,12 +64,12 @@ IF (UNIX AND NOT APPLE)
+   # Plugin-specific stuff, some distros set CMAKE_INSTALL_LIBDIR to
+   # /usr/lib64 (Fedora64, for example)
+   IF (NOT CMAKE_INSTALL_LIBDIR)
+-    SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib)
++    SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX})
+   ENDIF (NOT CMAKE_INSTALL_LIBDIR)
+   SET (MASSXPERT_PLUGIN_DIR ${CMAKE_INSTALL_LIBDIR}/massxpert/plugins)
+ 
+   SET (MASSXPERT_LOCALE_DIR ${CMAKE_INSTALL_PREFIX}/share/massxpert/locales)
+-  SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert)
++  SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert-${VERSION})
+   SET (MASSXPERT_USERMAN_DIR ${MASSXPERT_DOC_DIR}/usermanual)
+ ENDIF (UNIX AND NOT APPLE)
+ 
+@@ -144,10 +144,6 @@ IF (${BUILD_PROGRAM})
+   ###############
+   # install stuff
+ 
+-  # The license file
+-  INSTALL (FILES COPYING
+-    DESTINATION ${MASSXPERT_DOC_DIR})
+-
+   # The desktop file
+   IF (UNIX AND NOT APPLE)
+     INSTALL (FILES massxpert.desktop
+@@ -185,10 +181,6 @@ IF (${BUILD_DATA})
+   ###############
+   # install stuff
+   
+-  # The license file
+-  INSTALL (FILES COPYING
+-    DESTINATION ${MASSXPERT_DOC_DIR})
+-  
+   # The manual pages (data)
+   IF (UNIX AND NOT APPLE)
+     INSTALL (FILES massxpert-data.7
+@@ -219,10 +211,6 @@ IF (${BUILD_USERMANUAL})
+   ###############
+   # install stuff
+   
+-  # The license file
+-  INSTALL (FILES COPYING
+-    DESTINATION ${MASSXPERT_DOC_DIR})
+-  
+   # The manual pages (user manual)
+   IF (UNIX AND NOT APPLE)
+     INSTALL (FILES massxpert-doc.7
+diff --git a/gui/configurationSettingsDlg.cpp b/gui/configurationSettingsDlg.cpp
+index bf595d5..82cad21 100644
+--- a/gui/configurationSettingsDlg.cpp
++++ b/gui/configurationSettingsDlg.cpp
+@@ -309,13 +309,11 @@ namespace massXpert
+   bool 
+   ConfigurationSettingsDlg::checkLocalizationDir(const QDir &dir)
+   {
+-    // At the moment there is the french translation: massxpert_fr.qm
++    // Gentoo provides optional installing of translations.
++    // If you decide not to have translations, then this check
++    // would fail.
+ 
+-    QString filePath(dir.absolutePath() +
+-		      QDir::separator() +
+-		      "massxpert_fr.qm");
+-    
+-    return QFile::exists(filePath);
++    return true;
+   }
+   
+ 
diff --git a/sci-chemistry/massxpert/massxpert-1.7.6.ebuild b/sci-chemistry/massxpert/massxpert-1.7.6.ebuild
deleted file mode 100644
index 1ca048b8e286..000000000000
--- a/sci-chemistry/massxpert/massxpert-1.7.6.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/massxpert-1.7.6.ebuild,v 1.7 2013/03/02 23:18:07 hwoarang Exp $
-
-EAPI=2
-
-inherit base eutils flag-o-matic cmake-utils
-
-DESCRIPTION="A software suite to predict/analyze mass spectrometric data on (bio)polymers."
-HOMEPAGE="http://massxpert.org/wiki/"
-SRC_URI="http://download.tuxfamily.org/massxpert/source/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-RDEPEND="
-	dev-qt/qtgui:4[accessibility]
-	dev-qt/qtsvg:4
-	dev-qt/qtxmlpatterns:4
-	x11-libs/libSM
-	x11-libs/libICE
-	x11-libs/libXi
-	x11-libs/libXrender
-	x11-libs/libXrandr
-	x11-libs/libXcursor
-	x11-libs/libXext
-	x11-libs/libXt
-	x11-libs/libXfixes
-	x11-libs/libXau
-	x11-libs/libXdmcp
-	x11-libs/libX11
-	sys-libs/zlib
-	media-libs/freetype
-	media-libs/fontconfig
-	media-libs/nas
-	media-libs/libpng
-	dev-libs/libxml2:2"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/"${P}"
-CMAKE_IN_SOURCE_BUILD="true"
-
-PATCHES=( "${FILESDIR}/${P}-gcc43.patch" )
-
-src_compile() {
-	sed -i \
-		-e "s:/lib/:/$(get_libdir)/:g" \
-		-e "s:ADD_DEFINITIONS (-Wall -Werror):ADD_DEFINITIONS (-Wall):" \
-		CMakeLists.txt || \
-		die "404. File not found while sedding."
-
-	tc-export CC CXX LD
-	mycmakeargs="-D__LIB=$(get_libdir)"
-
-	if use amd64 ; then
-		append-flags -fPIC
-	fi
-
-	cmake-utils_src_compile
-}
diff --git a/sci-chemistry/massxpert/massxpert-2.0.5.ebuild b/sci-chemistry/massxpert/massxpert-2.0.5.ebuild
index 01f2f914a1ea..b0b1b7362cf4 100644
--- a/sci-chemistry/massxpert/massxpert-2.0.5.ebuild
+++ b/sci-chemistry/massxpert/massxpert-2.0.5.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/massxpert-2.0.5.ebuild,v 1.3 2013/03/02 23:18:07 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/massxpert-2.0.5.ebuild,v 1.4 2014/01/06 15:24:25 jlec Exp $
 
 EAPI="2"
 
@@ -40,12 +40,11 @@ src_prepare() {
 }
 
 src_configure() {
-	append-ldflags $(no-as-needed)
-
-	mycmakeargs="
+	local mycmakeargs=(
 		-DBUILD_PROGRAM=1
-		-DBUILD_DATA=1"
-	use doc && mycmakeargs="${mycmakeargs} -DBUILD_USERMANUAL=1"
+		-DBUILD_DATA=1
+	)
+	use doc && mycmakeargs+=( -DBUILD_USERMANUAL=1 )
 
 	cmake-utils_src_configure
 }
diff --git a/sci-chemistry/massxpert/massxpert-3.4.0.ebuild b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild
new file mode 100644
index 000000000000..9fb491e75931
--- /dev/null
+++ b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/massxpert/massxpert-3.4.0.ebuild,v 1.1 2014/01/06 15:24:25 jlec Exp $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Software suite to predict/analyze mass spectrometric data on (bio)polymers"
+HOMEPAGE="http://massxpert.org"
+SRC_URI="http://download.tuxfamily.org/${PN}/source/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc"
+
+RDEPEND="dev-qt/qtsvg:4[debug?]"
+DEPEND="${DEPEND}
+	doc? ( virtual/latex-base )"
+
+MASSXPERT_LANGS="fr"
+
+for L in ${MASSXPERT_LANGS}; do
+	IUSE="${IUSE} linguas_${L}"
+done
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-gentoo.patch"
+
+	local langs=
+	for lingua in ${LINGUAS}; do
+		if has ${lingua} ${MASSXPERT_LANGS}; then
+			langs="${langs} ${PN}_${lingua}.qm"
+		fi
+	done
+
+	sed -i -e "s/\(SET (massxpert_TRANSLATIONS \).*/\1${langs})/" \
+		gui/CMakeLists.txt || die "setting up translations failed"
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_PROGRAM=1
+		-DBUILD_DATA=1
+	)
+	use doc && mycmakeargs+=( -DBUILD_USERMANUAL=1 )
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	doicon "gui/images/${PN}-icon-32.xpm"
+	dodoc TODO
+}
diff --git a/sci-chemistry/massxpert/metadata.xml b/sci-chemistry/massxpert/metadata.xml
index 8f2a1a4dac00..a4137981114b 100644
--- a/sci-chemistry/massxpert/metadata.xml
+++ b/sci-chemistry/massxpert/metadata.xml
@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
-<email>je_fro@gentoo.org</email>
-<name>Jeff Gardner</name>
-</maintainer>
-<longdescription lang="en">
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>je_fro@gentoo.org</email>
+    <name>Jeff Gardner</name>
+  </maintainer>
+  <longdescription lang="en">
 Prediction and analysis of mass spectrometric data for proteomic projects.
 </longdescription>
 </pkgmetadata>
-