Merge branch 'master' of https://github.com/gentoo-science/sci

12 files changed, 467 insertions, 59 deletions

diff --git a/dev-python/Forthon/Forthon-0.8.10.ebuild b/dev-python/Forthon/Forthon-0.8.11.ebuild
index f1fa4ed20..2383f9bca 100644
--- a/dev-python/Forthon/Forthon-0.8.10.ebuild
+++ b/dev-python/Forthon/Forthon-0.8.11.ebuild
@@ -2,32 +2,30 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
+PYTHON_COMPAT=( python{2_5,2_6,2_7,3_1,3_2,3_3} )
 
-PYTHON_DEPEND="*"
-SUPPORT_PYTHON_ABIS="1"
-
-inherit distutils
+inherit distutils-r1
 
 DESCRIPTION="Python interface generator for Fortran based codes"
 HOMEPAGE="http://hifweb.lbl.gov/Forthon http://pypi.python.org/pypi/Forthon"
 SRC_URI="http://hifweb.lbl.gov/${PN}/${P}.tgz"
 
-LICENSE="BSD"
+LICENSE="LLNL-BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="examples"
 
-src_prepare() {
-	sed -i -e "s/'Notice',//" setup.py || die
-	distutils_src_prepare
+python_prepare_all() {
+	sed -i -e "/data_files/ s/'License.txt',//" setup.py || die
+	distutils-r1_python_prepare_all
 }
 
-src_install() {
-	distutils_src_install
+python_install_all() {
 	dohtml docs/index.html
 	if use examples ; then
 		insinto /usr/share/doc/${PF}
 		doins -r {example,example2,simpleexample}
 	fi
+	distutils-r1_python_install_all
 }
diff --git a/dev-python/Forthon/Manifest b/dev-python/Forthon/Manifest
index 25603197e..2bf5db228 100644
--- a/dev-python/Forthon/Manifest
+++ b/dev-python/Forthon/Manifest
@@ -1 +1 @@
-DIST Forthon-0.8.10.tgz 89048 SHA256 a92236a1dbdc87f7235247555467216d2db0994db37275fa434775f64b690de4 SHA512 1332e3d5465ca249c357314cf15d2a4e5e83a941841021b8f6a17a107dce268a7a082838ade5e8db944ecde6bfb111211ab218aa414ee90aafbb81f1491b3b93 WHIRLPOOL 9a617dfce840179bcc079b230bfad893c24a915357cf1c3ddca85dfafe6ebe8ccda8106f3ee27db5c9ecc9764ebfe0a7a403a14d731bf90e1173bf777ec771ba
+DIST Forthon-0.8.11.tgz 89277 SHA256 cba78e0f392e75f46a61084b3b16970c9f5828bbd57010bed5e2301002dcbfed SHA512 3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 WHIRLPOOL 4235e4c3e9a1a2dcc2b3a9250464c9d77b13cacb3f339abc2938979def06272ab6a9145319a4a249ed32419521024841f622af2601395ba981e37dd60a20fe08
diff --git a/licenses/LNLL-BSD b/licenses/LNLL-BSD
new file mode 100644
index 000000000..5d9e89279
--- /dev/null
+++ b/licenses/LNLL-BSD
@@ -0,0 +1,57 @@
+Copyright (c) 2012, Lawrence Livermore National Security, LLC.
+Produced at the Lawrence Livermore National Laboratory
+Written by David Grote, grote1@llnl.gov.
+LLNL-CODE-544231
+All rights reserved.
+
+This file is part of Forthon. For details, see http://hifweb.lbl.gov/Forthon.
+Please also read below, an Additional BSD Notice.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+   * Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the disclaimer below.
+
+   * Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the disclaimer (as noted below) in
+     the documentation and/or other materials provided with the distribution.
+
+   * Neither the name of the LLNS/LLNL nor the names of its contributors may
+     be used to endorse or promote products derived from this software
+     without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY, LLC,
+THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Additional BSD Notice
+
+1. This notice is required to be provided under our contract with the U.S.
+Department of Energy (DOE). This work was produced at Lawrence Livermore
+National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
+
+2. Neither the United States Government nor Lawrence Livermore National
+Security, LLC nor any of their employees, makes any warranty, express or
+implied, or assumes any liability or responsibility for the accuracy,
+completeness, or usefulness of any information, apparatus, product, or
+process disclosed, or represents that its use would not infringe
+privately-owned rights.
+
+3. Also, reference herein to any specific commercial products, process, or
+services by trade name, trademark, manufacturer or otherwise does not
+necessarily constitute or imply its endorsement, recommendation, or favoring
+by the United States Government or Lawrence Livermore National Security, LLC.
+The views and opinions of authors expressed herein do not necessarily state
+or reflect those of the United States Government or Lawrence Livermore
+National Security, LLC, and shall not be used for advertising or product
+endorsement purposes.
+
diff --git a/profiles/package.mask b/profiles/package.mask
index 9953a7d9c..5c8ce2c4f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,13 +30,6 @@
 
 #--- END OF EXAMPLES ---
 
-# Guillaume Horel <guillaume.horel@gmail.com> (11 July 2012)
-# masked for upcoming scilab-5.4.0
-=sci-mathematics/scilab-5.4.0
-=dev-java/jrosetta-1.0.4
-=dev-java/flexdock-1.2.0
->=dev-java/jgraphx-1.8
-
 # Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
 # live ebuild
 =sci-chemistry/freeon-9999
diff --git a/sci-biology/psychopy/metadata.xml b/sci-biology/psychopy/metadata.xml
new file mode 100644
index 000000000..c791a24ff
--- /dev/null
+++ b/sci-biology/psychopy/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>h.chr@mail.ru</email>
+		<name>TheChymera</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/psychopy/psychopy-1.75.01.ebuild b/sci-biology/psychopy/psychopy-1.75.01.ebuild
index 9d6b51dee..ee50eb007 100644
--- a/sci-biology/psychopy/psychopy-1.75.01.ebuild
+++ b/sci-biology/psychopy/psychopy-1.75.01.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -23,16 +23,16 @@ KEYWORDS="~amd64 ~x86"
 IUSE="test"
 
 RDEPEND="dev-python/numpy[lapack]
-        sci-libs/scipy
-        dev-python/matplotlib
-        dev-python/pyopengl[${PYTHON_USEDEP}]
-        dev-python/imaging
-        dev-python/wxpython
-        dev-python/setuptools[${PYTHON_USEDEP}]
-        dev-python/lxml[${PYTHON_USEDEP}]
-        app-admin/eselect
-        dev-python/pyglet
-        dev-python/pygame"
+	sci-libs/scipy
+	dev-python/matplotlib
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/imaging
+	dev-python/wxpython
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/lxml[${PYTHON_USEDEP}]
+	app-admin/eselect
+	dev-python/pyglet
+	dev-python/pygame"
 
 DEPEND="app-arch/unzip
 	dev-python/setuptools
@@ -43,9 +43,9 @@ RESTRICT="test" # interactive, opens lots of windows
 S="${WORKDIR}/${MY_P}"
 
 python_install_all() {
-        distutils-r1_python_install_all
-        doicon psychopy/monitors/psychopy.ico
-        make_desktop_entry psychopyapp.py PsychoPy psychopy "Science;Biology"
+	distutils-r1_python_install_all
+	doicon psychopy/monitors/psychopy.ico
+	make_desktop_entry psychopyapp.py PsychoPy psychopy "Science;Biology"
 }
 
 pkg_postinst() {
diff --git a/sci-biology/psychopy/psychopy-9999.ebuild b/sci-biology/psychopy/psychopy-9999.ebuild
index 88b339356..751129304 100644
--- a/sci-biology/psychopy/psychopy-9999.ebuild
+++ b/sci-biology/psychopy/psychopy-9999.ebuild
@@ -5,7 +5,7 @@
 EAPI="5"
 PYTHON_COMPAT=( python2_7 )
 
-inherit eutils gnome2-eutils distutils-r1 git-2
+inherit eutils gnome2-utils distutils-r1 git-2
 
 DESCRIPTION="Python experiemntal psychology toolkit"
 HOMEPAGE="http://www.psychopy.org/"
@@ -22,16 +22,16 @@ RDEPEND="${DEPEND}
 	dev-python/lxml[${PYTHON_USEDEP}]
 	dev-python/matplotlib
 	dev-python/numpy[lapack]
-        dev-python/pygame
+	dev-python/pygame
 	dev-python/pyglet
 	dev-python/pyopengl[${PYTHON_USEDEP}]
 	dev-python/wxpython
 	sci-libs/scipy"
 
 python_install_all() {
-        distutils-r1_python_install_all
-        newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
-        make_desktop_entry psychopyApp.py PsychoPy psychopy "Science;Biology"
+	distutils-r1_python_install_all
+	newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg
+	make_desktop_entry psychopyApp.py PsychoPy psychopy "Science;Biology"
 }
 
 pkg_postinst() {
diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog
index 22266c7ef..dd11fd375 100644
--- a/sci-libs/atlas/ChangeLog
+++ b/sci-libs/atlas/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-libs/atlas
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*atlas-3.10.1 (28 Jan 2013)
+
+  28 Jan 2013; Sébastien Fabbro <bicatali@gentoo.org> +atlas-3.10.1.ebuild,
+  -atlas-3.10.0.ebuild:
+  sci-libs/atlas: Version bump
+
   12 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.8.4.ebuild,
   -files/3.9.39-bfr-overflow.patch, atlas-3.10.0.ebuild, metadata.xml:
   sci-libs/atlas: Update for lapack-3.4.2
diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest
index 05407be9f..70dc35a62 100644
--- a/sci-libs/atlas/Manifest
+++ b/sci-libs/atlas/Manifest
@@ -1,2 +1,2 @@
-DIST atlas3.10.0.tar.bz2 5025190 SHA256 a90a2e3463504e3297b56edc13769d766732e82bd8f1de951cfc78444f148465 SHA512 9aca9b5df322f17e80bcddc7e684b34954afbd91fefc701486604aa8f8da8dc709a781d96145f3d4cc60ec4985e96d892021bd3c9e5cba98bfa2ff2f5ae1f3eb WHIRLPOOL cce85bb3323574441143b4e33879607854b39a9d73c5cf8b043f32a26fd845da0d77d4a70d7a0280e63d2f94d9f6f048e7e9ef391907e710d5525ffcae1e2bd9
+DIST atlas3.10.1.tar.bz2 4900179 SHA256 a215b492204aae0205f4028e7c4076492a5d6a564f8f859ff062fd79587bcc86 SHA512 027c8eea79bc584a4586e198fd9cc0ef7fffda3983082c11c2cf618837a24ba25cb26a831f55c35ac9a425e1b4bd1f379c62d99ef0c4e060bc4b1de59f3cf5fc WHIRLPOOL 0d88934e1b1c050f987dfb370043af3b36a277341d66eff854789d1017a09f60234bead6bda01682a675d00277610af35d05e037d3f9425871b66c9f54d2e5e1
 DIST lapack-3.4.2.tgz 6168281 SHA256 60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0 SHA512 8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 WHIRLPOOL ca1333abaed2377e29acd08feee58241ba63b981ac5946dd9da663ed9c760e476ec3933a4989a964a66f5aaa72c868cd7f274259bc0dde0299d63fe60a3139fa
diff --git a/sci-libs/atlas/atlas-3.10.0.ebuild b/sci-libs/atlas/atlas-3.10.1.ebuild
index 2d9a170ab..d9da19eed 100644
--- a/sci-libs/atlas/atlas-3.10.0.ebuild
+++ b/sci-libs/atlas/atlas-3.10.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 FORTRAN_NEEDED=fortran
 inherit eutils toolchain-funcs fortran-2 versionator alternatives-2 multilib
@@ -49,7 +49,7 @@ pkg_setup() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-x32-support.patch
+	epatch "${FILESDIR}"/${PN}-3.10.0-x32-support.patch
 }
 
 src_configure() {
@@ -94,8 +94,6 @@ src_configure() {
 			myconf+=( "-b 32" )
 		elif use ia64; then
 			myconf+=( "-b 64" )
-		else #hppa alpha ...
-			myconf+=( "" )
 		fi
 		if use fortran; then
 			myconf+=(
@@ -236,6 +234,7 @@ src_install() {
 
 	if use fortran; then
 		LINK=$(tc-getF77) PCREQ=
+
 		# blas
 		atlas_install_libs libf77blas.a -lm -L. -latlas
 		atlas_install_pc f77blas atlas-blas -lm -latlas
diff --git a/sci-mathematics/scilab/files/scilab-5.4.0-builddocs.patch b/sci-mathematics/scilab/files/scilab-5.4.0-builddocs.patch
new file mode 100644
index 000000000..981bc9ba1
--- /dev/null
+++ b/sci-mathematics/scilab/files/scilab-5.4.0-builddocs.patch
@@ -0,0 +1,353 @@
+diff --git a/scilab/modules/core/src/c/callDynamicGateway.c b/scilab/modules/core/src/c/callDynamicGateway.c
+index 91439a9..7485f4c 100644
+--- a/scilab/modules/core/src/c/callDynamicGateway.c
++++ b/scilab/modules/core/src/c/callDynamicGateway.c
+@@ -3,11 +3,11 @@
+  * Copyright (C) 2008 - INRIA - Allan CORNET
+  * Copyright (C) 2008 - INRIA - Sylvestre LEDRU
+  * Copyright (C) 2010 - DIGITEO - Allan CORNET
+- * 
++ *
+  * This file must be used under the terms of the CeCILL.
+  * This source file is licensed as described in the file COPYING, which
+  * you should have received as part of this distribution.  The terms
+- * are also available at    
++ * are also available at
+  * http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt
+  *
+  */
+@@ -26,19 +26,18 @@
+ #include "charEncoding.h"
+ /*--------------------------------------------------------------------------*/
+ dynamic_gateway_error_code callDynamicGateway(char *moduleName,
+-                                              char *dynLibName,
+-                                              char *gw_name,
+-                                              DynLibHandle *hlib,
+-                                              PROC_GATEWAY *ptrGateway)
++        char *dynLibName,
++        char *gw_name,
++        DynLibHandle *hlib,
++        PROC_GATEWAY *ptrGateway)
+ {
+     if (*hlib == NULL)
+     {
+-        /* Under Linux/Unix, load thanks to dlopen */
+ #ifdef _MSC_VER
+         wchar_t *wcdynLibName = to_wide_string(dynLibName);
+         if (wcdynLibName)
+         {
+-            *hlib = LoadDynLibraryW(wcdynLibName); 
++            *hlib = LoadDynLibraryW(wcdynLibName);
+             FREE(wcdynLibName);
+             wcdynLibName = NULL;
+         }
+@@ -47,52 +46,73 @@ dynamic_gateway_error_code callDynamicGateway(char *moduleName,
+             return DYN_GW_LOAD_LIBRARY_ERROR;
+         }
+ #else
+-        *hlib = LoadDynLibrary(dynLibName); 
+ 
+-        if (*hlib == NULL) 
+-        {
+-            char *previousError = GetLastDynLibError();
+-
+-            /* Haven't been able to find the lib with dlopen... 
+-            * This can happen for two reasons:
+-            * - the lib must be dynamically linked
+-            * - Some silly issues under Suse (see bug #2875)
+-            * Note that we are handling only the "source tree build"
+-            * because libraries are split (they are in the same directory 
+-            * in the binary)
+-            */
+-            char *SciPath = getSCIpath();
++        /* First step, we are considering that we are in the source tree.
++         * Therefor, the lib should be in modules/xxx/.libs/
++         *
++         * Otherwise, dlopen will search in various places (for example, the install specified
++         * by --prefix).
++         * This leads to serious and unexpected bugs like #8883
++         * The original bug report for this issue was the bug #2875
++         */
++        char *SciPath = getSCIpath();
+ #define PATHTOMODULE "/modules/"
+ #ifndef LT_OBJDIR
+ #define LT_OBJDIR ".libs/"
+ #endif
+ 
+-            /* Build the full path to the library */
+-            char *pathToLib=(char*) MALLOC((strlen(SciPath)+strlen(PATHTOMODULE)+strlen(moduleName)+strlen("/")+strlen(LT_OBJDIR)+strlen(dynLibName)+1)*sizeof(char));
+-            sprintf(pathToLib,"%s%s%s/%s%s",SciPath,PATHTOMODULE,moduleName,LT_OBJDIR,dynLibName);
++        /* Build the full path to the library */
++        char *pathToLib = (char*) MALLOC((strlen(SciPath) + strlen(PATHTOMODULE) + strlen(moduleName) + strlen("/") + strlen(LT_OBJDIR) + strlen(dynLibName) + 1) * sizeof(char));
++        sprintf(pathToLib, "%s%s%s/%s%s", SciPath, PATHTOMODULE, moduleName, LT_OBJDIR, dynLibName);
+ 
+-            *hlib = LoadDynLibrary(pathToLib);
++        /* Load the library with the Scilab source-tree paths */
++        *hlib = LoadDynLibrary(pathToLib);
++
++        if (*hlib == NULL) /* Load of the hardcoded path to the lib failed */
++        {
+ 
+-            if (*hlib == NULL) 
++            /* Under Linux/Unix, load thanks to dlopen on the system.
++             * In the binary, the LD_LIBRARY_PATH is declared in the startup script (ie bin/scilab*)
++             * Note that it is not possible to update the LD_LIBRARY_PATH at run time.
++             */
++            *hlib = LoadDynLibrary(dynLibName);
++            if (*hlib == NULL)
+             {
++                char *previousError = GetLastDynLibError();
+                 if (previousError != NULL)
+                 {
+-                    sciprint("A previous error has been detected while loading %s: %s\n",dynLibName, previousError);
++                    sciprint("A previous error has been detected while loading %s: %s\n", dynLibName, previousError);
++                }
++                if (SciPath)
++                {
++                    FREE(SciPath);
++                    SciPath = NULL;
++                }
++                if (pathToLib)
++                {
++                    FREE(pathToLib);
++                    pathToLib = NULL;
+                 }
+-                if (SciPath) {FREE(SciPath); SciPath = NULL;}
+-                if (pathToLib) {FREE(pathToLib); pathToLib = NULL;}
+                 return DYN_GW_LOAD_LIBRARY_ERROR;
+             }
+-            if (SciPath) {FREE(SciPath); SciPath = NULL;}
+-            if (pathToLib) {FREE(pathToLib); pathToLib = NULL;}
++        }
++        if (SciPath)
++        {
++            FREE(SciPath);
++            SciPath = NULL;
++        }
++        if (pathToLib)
++        {
++            FREE(pathToLib);
++            pathToLib = NULL;
+         }
+ #endif
+     }
+ 
+     if (*ptrGateway == NULL)
+     {
+-        *ptrGateway = (PROC_GATEWAY) GetDynLibFuncPtr(*hlib,gw_name);
+-        if (*ptrGateway == NULL) 
++        *ptrGateway = (PROC_GATEWAY) GetDynLibFuncPtr(*hlib, gw_name);
++        if (*ptrGateway == NULL)
+         {
+             return DYN_GW_PTR_FUNCTION_ERROR ;
+         }
+@@ -110,49 +130,50 @@ dynamic_gateway_error_code callDynamicGateway(char *moduleName,
+ char *buildModuleDynLibraryName(char *modulename, dynlib_name_format iType)
+ {
+     char *dynlibname = NULL;
+-    int lenName = (int)(strlen(modulename)+strlen(SHARED_LIB_EXT));
++    int lenName = (int)(strlen(modulename) + strlen(SHARED_LIB_EXT));
+     switch (iType)
+     {
+-    case DYNLIB_NAME_FORMAT_AUTO: default:
++        case DYNLIB_NAME_FORMAT_AUTO:
++        default:
+ #ifdef _MSC_VER
+-        lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_1);
++            lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_1);
+ #else
+-        lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_3);
++            lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_3);
+ #endif
+-        dynlibname = (char*)MALLOC(sizeof(char)*(lenName+1));
+-        if (dynlibname)
+-        {
++            dynlibname = (char*)MALLOC(sizeof(char) * (lenName + 1));
++            if (dynlibname)
++            {
+ #ifdef _MSC_VER
+-            sprintf(dynlibname,FORMATGATEWAYLIBNAME_1,modulename,SHARED_LIB_EXT);
++                sprintf(dynlibname, FORMATGATEWAYLIBNAME_1, modulename, SHARED_LIB_EXT);
+ #else
+-            sprintf(dynlibname,FORMATGATEWAYLIBNAME_3,modulename,SHARED_LIB_EXT);
++                sprintf(dynlibname, FORMATGATEWAYLIBNAME_3, modulename, SHARED_LIB_EXT);
+ #endif
+-        }
+-        break;
+-    case DYNLIB_NAME_FORMAT_1:
+-        lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_1);
+-        dynlibname = (char*)MALLOC(sizeof(char)*(lenName+1));
+-        if (dynlibname)
+-        {
+-            sprintf(dynlibname,FORMATGATEWAYLIBNAME_1,modulename,SHARED_LIB_EXT);
+-        }
+-        break;
+-    case DYNLIB_NAME_FORMAT_2:
+-        lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_2);
+-        dynlibname = (char*)MALLOC(sizeof(char)*(lenName+1));
+-        if (dynlibname)
+-        {
+-            sprintf(dynlibname,FORMATGATEWAYLIBNAME_2,modulename,SHARED_LIB_EXT);
+-        }
+-        break;
+-    case DYNLIB_NAME_FORMAT_3:
+-        lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_3);
+-        dynlibname = (char*)MALLOC(sizeof(char)*(lenName+1));
+-        if (dynlibname)
+-        {
+-            sprintf(dynlibname,FORMATGATEWAYLIBNAME_3,modulename,SHARED_LIB_EXT);
+-        }
+-        break;
++            }
++            break;
++        case DYNLIB_NAME_FORMAT_1:
++            lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_1);
++            dynlibname = (char*)MALLOC(sizeof(char) * (lenName + 1));
++            if (dynlibname)
++            {
++                sprintf(dynlibname, FORMATGATEWAYLIBNAME_1, modulename, SHARED_LIB_EXT);
++            }
++            break;
++        case DYNLIB_NAME_FORMAT_2:
++            lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_2);
++            dynlibname = (char*)MALLOC(sizeof(char) * (lenName + 1));
++            if (dynlibname)
++            {
++                sprintf(dynlibname, FORMATGATEWAYLIBNAME_2, modulename, SHARED_LIB_EXT);
++            }
++            break;
++        case DYNLIB_NAME_FORMAT_3:
++            lenName = lenName + (int)strlen(FORMATGATEWAYLIBNAME_3);
++            dynlibname = (char*)MALLOC(sizeof(char) * (lenName + 1));
++            if (dynlibname)
++            {
++                sprintf(dynlibname, FORMATGATEWAYLIBNAME_3, modulename, SHARED_LIB_EXT);
++            }
++            break;
+     }
+     return dynlibname;
+ }
+@@ -160,36 +181,36 @@ char *buildModuleDynLibraryName(char *modulename, dynlib_name_format iType)
+ char *buildGatewayName(char *modulename)
+ {
+     /* example gw_scicos */
+-#define FORMATGATEWAYNAME "gw_%s" 
++#define FORMATGATEWAYNAME "gw_%s"
+ 
+     char *gatewayname = NULL;
+-    int lenName = (int)(strlen(modulename)+strlen(FORMATGATEWAYNAME));
+-    gatewayname = (char*)MALLOC(sizeof(char)*(lenName+1));
++    int lenName = (int)(strlen(modulename) + strlen(FORMATGATEWAYNAME));
++    gatewayname = (char*)MALLOC(sizeof(char) * (lenName + 1));
+ 
+     if (gatewayname)
+     {
+-        sprintf(gatewayname,FORMATGATEWAYNAME,modulename);
++        sprintf(gatewayname, FORMATGATEWAYNAME, modulename);
+     }
+ 
+     return gatewayname;
+ }
+ /*--------------------------------------------------------------------------*/
+-void displayErrorGateway(dynamic_gateway_error_code err,char *libraryname,char *functionname)
++void displayErrorGateway(dynamic_gateway_error_code err, char *libraryname, char *functionname)
+ {
+     switch (err)
+     {
+-    case DYN_GW_NO_ERROR :
+-        /* NO ERROR */
+-        break;
+-    case DYN_GW_LOAD_LIBRARY_ERROR :
+-        Scierror(999,_("Impossible to load %s library: %s\n"),libraryname,GetLastDynLibError());
+-        break;
+-    case DYN_GW_PTR_FUNCTION_ERROR :
+-        Scierror(999,_("Impossible to load %s function in %s library: %s\n"),functionname,libraryname, GetLastDynLibError());
+-        break;
+-    case DYN_GW_CALL_FUNCTION_ERROR :
+-        Scierror(999,_("Impossible to call %s in %s library: %s\n"),functionname,libraryname,GetLastDynLibError());
+-        break;
++        case DYN_GW_NO_ERROR :
++            /* NO ERROR */
++            break;
++        case DYN_GW_LOAD_LIBRARY_ERROR :
++            Scierror(999, _("Impossible to load %s library: %s\n"), libraryname, GetLastDynLibError());
++            break;
++        case DYN_GW_PTR_FUNCTION_ERROR :
++            Scierror(999, _("Impossible to load %s function in %s library: %s\n"), functionname, libraryname, GetLastDynLibError());
++            break;
++        case DYN_GW_CALL_FUNCTION_ERROR :
++            Scierror(999, _("Impossible to call %s in %s library: %s\n"), functionname, libraryname, GetLastDynLibError());
++            break;
+     }
+ }
+ /*--------------------------------------------------------------------------*/
+diff --git a/scilab/modules/core/src/c/gw_dynamic_generic.c b/scilab/modules/core/src/c/gw_dynamic_generic.c
+index e146235..09eb88d 100644
+--- a/scilab/modules/core/src/c/gw_dynamic_generic.c
++++ b/scilab/modules/core/src/c/gw_dynamic_generic.c
+@@ -1,11 +1,11 @@
+ /*
+  * Scilab ( http://www.scilab.org/ ) - This file is part of Scilab
+  * Copyright (C) 2008 - INRIA - Allan CORNET
+- * 
++ *
+  * This file must be used under the terms of the CeCILL.
+  * This source file is licensed as described in the file COPYING, which
+  * you should have received as part of this distribution.  The terms
+- * are also available at    
++ * are also available at
+  * http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt
+  *
+  */
+@@ -15,28 +15,28 @@
+ #include "gw_dynamic_generic.h"
+ /*--------------------------------------------------------------------------*/
+ int gw_dynamic_generic(char *moduleName,
+-					   char **dynlibName,
+-					   char **gatewayName,
+-					   DynLibHandle *hModuleLib,
+-					   PROC_GATEWAY *ptrGatewayFunction)
++                       char **dynlibName,
++                       char **gatewayName,
++                       DynLibHandle *hModuleLib,
++                       PROC_GATEWAY *ptrGatewayFunction)
+ {
+-	dynamic_gateway_error_code err;
+-	if (*dynlibName == NULL)
+-	{
+-		*dynlibName = buildModuleDynLibraryName(moduleName, DYNLIB_NAME_FORMAT_AUTO);
+-	}
++    dynamic_gateway_error_code err;
++    if (*dynlibName == NULL)
++    {
++        *dynlibName = buildModuleDynLibraryName(moduleName, DYNLIB_NAME_FORMAT_AUTO);
++    }
++
++    if (*gatewayName == NULL)
++    {
++        *gatewayName = buildGatewayName(moduleName);
++    }
+ 
+-	if (*gatewayName == NULL)
+-	{
+-		*gatewayName = buildGatewayName(moduleName);
+-	}
++    err = callDynamicGateway(moduleName, *dynlibName,
++                             *gatewayName,
++                             hModuleLib,
++                             ptrGatewayFunction);
++    displayErrorGateway(err, *dynlibName, *gatewayName);
+ 
+-	err = callDynamicGateway(moduleName,*dynlibName,
+-							*gatewayName,
+-							hModuleLib,
+-							ptrGatewayFunction);
+-	displayErrorGateway(err,*dynlibName,*gatewayName);
+-	
+-	return 0;
++    return 0;
+ }
+ /*--------------------------------------------------------------------------*/
+-- 
+1.7.9.5
+
diff --git a/sci-mathematics/scilab/scilab-5.4.0.ebuild b/sci-mathematics/scilab/scilab-5.4.0.ebuild
index d62611f08..f5616379e 100644
--- a/sci-mathematics/scilab/scilab-5.4.0.ebuild
+++ b/sci-mathematics/scilab/scilab-5.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,15 +10,9 @@ VIRTUALX_REQUIRED="manual"
 inherit eutils autotools bash-completion-r1 check-reqs fdo-mime flag-o-matic \
 	fortran-2 java-pkg-opt-2 toolchain-funcs virtualx
 
-# Comments:
-# - we don't rely on the configure script to find the right version of java
-# packages. This should fix bug #41821
 # Things that don't work:
 # - tests
 # - can't build without docs (-doc) 
-# - has to call eautoconf, and not eautoreconf, libtool fails otherwise
-# - needs to remove scilab-5.3.x before installing otherwise gets a DOCBOOK_ROOT
-# error
 
 DESCRIPTION="Scientific software package for numerical computations"
 LICENSE="CeCILL-2"
@@ -116,7 +110,6 @@ pkg_setup() {
 	for l in ${LINGUASLONG}; do
 		use linguas_${l%_*} && ALL_LINGUAS="${ALL_LINGUAS} ${l}"
 	done
-
 	export ALL_LINGUAS ALL_LINGUAS_DOC=$ALL_LINGUAS
 }
 
@@ -125,20 +118,20 @@ src_prepare() {
 		"${FILESDIR}/${P}-fortran-link.patch" \
 		"${FILESDIR}/${P}-followlinks.patch" \
 		"${FILESDIR}/${P}-gluegen.patch" \
-		"${FILESDIR}/${P}-fix-random-runtime-failure.patch"
+		"${FILESDIR}/${P}-fix-random-runtime-failure.patch" \
+		"${FILESDIR}/${P}-builddocs.patch"
 
 	append-ldflags $(no-as-needed)
 
 	# increases java heap to 512M when building docs (sync with cheqreqs above)
 	use doc && epatch "${FILESDIR}/${P}-java-heap.patch"
 
+	# use the LINGUAS variable that we set
 	sed -i -e "/^ALL_LINGUAS=/d" -e "/^ALL_LINGUAS_DOC=/d" -i configure.ac
-	# make sure library path are preloaded in binaries
-	sed -i \
-		-e "s|^LD_LIBRARY_PATH=|LD_LIBRARY_PATH=${EPREFIX}/usr/$(get_libdir)/scilab:|g" \
-		bin/scilab* || die
-	# make sure it exports the DOCBOOK_ROOT variable
+
+	# make sure the DOCBOOK_ROOT variable is set
 	sed -i -e "s/xsl-stylesheets-\*/xsl-stylesheets/g" bin/scilab* || die
+
 	#add specific gentoo java directories
 	if use gui; then
 		sed -i -e "s|/usr/lib/jogl|/usr/lib/jogl-2|" \
@@ -151,6 +144,7 @@ src_prepare() {
 		sed -i -e "s/jogl/jogl-2/" -e "s/gluegen/gluegen-2/" \
 			etc/librarypath.xml || die
 	fi
+
 	mkdir jar || die
 	pushd jar
 	java-pkg_jar-from jgraphx-1.8,jlatexmath-1,flexdock,skinlf