Update sage

atlas-lapack/PKGBUILD

@@ -0,0 +1,109 @@
+#
+# Platform packages for Chakra
+#
+
+pkgname=atlas-lapack
+pkgver=3.8.4
+_lapackver=3.4.0
+pkgrel=1
+pkgdesc="Complete LAPACK and BLAS implementation using optimised ATLAS routines"
+url="http://math-atlas.sourceforge.net/"
+depends=('gcc-libs')
+makedepends=('binutils' 'sed' 'gcc-fortran')
+arch=('i686' 'x86_64')
+conflicts=('blas' 'lapack' 'cblas')
+provides=("blas" "lapack=$_lapackver" 'cblas')
+license=('custom:blas' 'custom:lapack' 'custom:atlas')
+source=(http://www.netlib.org/lapack/lapack-$_lapackver.tgz http://downloads.sourceforge.net/math-atlas/atlas${pkgver}.tar.bz2 blas-license.txt atlas-license.txt lapack.patch makefile.shared.mt makefile.shared.st misdetects_i1_as_i2.patch)
+md5sums=('02d5706ec03ba885fc246e5fa10d8c70'
+         '1bb3abde499b492b4be1f1a0759fbfa2'
+         '38b6acb8ed5691d25863319d30a8b365'
+         '4903eb06072dfbf94710691ccb6660bf'
+         'c681f11a9e17d31247570a26e266a506'
+         '235db0272fc5a17100115d5c45f29700'
+         '16691a5b602dcb5a20abc525b2ae9cfc'
+         '628b8f61b0403f23558ce6bf4c723bbc')
+
+build() {
+
+   NCPU=`grep "^processor" /proc/cpuinfo | wc -l`
+   [ -x /usr/bin/cpufreq-info ] && [ $(cpufreq-info -d) != '' ] && {
+       ICPU=0
+       while [ $ICPU -lt $NCPU ]; do
+          STATUS=`cpufreq-info -c $ICPU -p | cut -d' ' -f3`
+          [ "$STATUS" != "performance" ] && {
+             msg 'Before building this package, as root you must run'
+             msg '"cpufreq-set -g performance -c <CPU nr>" for each CPU (<CPU'
+             msg 'nr> is 0, 1, 2 up to the number of your CPUS.'
+             return 1
+          }
+          let ICPU=ICPU+1
+       done
+   }
+   if [ "$CARCH" = "x86_64" ]; then
+      ARCHITECTURE_BUILD_OPTS="-b 64" # for x86_64
+   else
+      ARCHITECTURE_BUILD_OPTS="-b 32" # for i686
+   fi
+
+   mkdir -p "$srcdir/ATLAS/build"
+   cd "$srcdir/ATLAS"
+   patch -p0 -i "$srcdir/misdetects_i1_as_i2.patch"
+   cd "$srcdir/ATLAS/build"
+
+   msg 'Determine compiler and options for LAPACK'
+   ../configure --prefix=/usr/ $ARCHITECTURE_BUILD_OPTS -Fa alg -fPIC
+   FORTRAN=`grep "F77 =" Make.inc|sed -e 's/ *F77 = //'`
+   FORTRANOPS=`grep "F77FLAGS =" Make.inc|sed -e 's/ *F77FLAGS = //'`
+   NOPTS=`echo $FORTRANOPS|sed -e 's/-O[0-9]/-O0/'`
+
+   msg 'Build LAPACK'
+   cd "$srcdir/lapack-$_lapackver"
+   cp INSTALL/make.inc.gfortran make.inc
+   patch -Np0 -i "$srcdir/lapack.patch"
+   make FORTRAN=$FORTRAN OPTS="$FORTRANOPS" NOOPT="$NOPTS" lib
+   LAPACKLIB="$srcdir/lapack-$_lapackver/liblapack.a"
+
+   msg 'Build ATLAS'
+   cd "$srcdir/ATLAS/build"
+   rm -rf *
+   ../configure --prefix=/usr/ $ARCHITECTURE_BUILD_OPTS -Fa alg -fPIC \
+      --with-netlib-lapack="$LAPACKLIB"
+   make -j1 build
+   make -j1 check
+   make -j1 time
+   msg 'Build shared libraries'
+   cd lib
+   if [ 1 -lt $NCPU ]; then
+      cp "$srcdir/makefile.shared.mt" makefile
+   else
+      cp "$srcdir/makefile.shared.st" makefile
+   fi
+   make -f makefile
+}
+
+package() {
+
+   NCPU=`grep "^processor" /proc/cpuinfo | wc -l`
+
+   cd "$srcdir/ATLAS/build"
+   make DESTDIR="$pkgdir/usr" install
+   cp -d lib/*.so* "$pkgdir/usr/lib"
+   cd "$pkgdir/usr/lib"
+   if [ 1 -lt $NCPU ]; then
+      mv -f libptcblas.a libcblas.a
+      mv -f libptf77blas.a libf77blas.a
+   else
+      rm -f *pt*
+   fi
+   ln -s libf77blas.so libblas.so.3
+   ln -s liblapack.so.$_lapackver liblapack.so.3
+   ln -s liblapack.so.3 liblapack.so
+
+   install -Dm644 "${srcdir}/blas-license.txt" \
+      "${pkgdir}/usr/share/licenses/$pkgname/blas-license.txt"
+   install -Dm644 "${srcdir}/lapack-$_lapackver/LICENSE" \
+      "${pkgdir}/usr/share/licenses/$pkgname/lapack-license.txt"
+   install -Dm644 "${srcdir}/atlas-license.txt" \
+      "${pkgdir}/usr/share/licenses/$pkgname/atlas-license.txt"
+}

atlas-lapack/atlas-license.txt

@@ -0,0 +1,29 @@
+             Automatically Tuned Linear Algebra Software v3.8.2
+                    (C) Copyright 1999 R. Clint Whaley
+
+ Code contributers : R. Clint Whaley, Antoine P. Petitet
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions, and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+   3. The name of the ATLAS group or the names of its contributers may
+      not be used to endorse or promote products derived from this
+      software without specific 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 THE ATLAS GROUP OR ITS 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.
+ 

atlas-lapack/blas-license.txt

@@ -0,0 +1,19 @@
+From: http://www.netlib.org/blas/faq.html
+
+ 2) Are there legal restrictions on the use of BLAS reference
+    implementation software? 
+
+The reference BLAS is a freely-available software package. It is
+available from netlib via anonymous ftp and the World Wide Web. Thus,
+it can be included in commercial software packages (and has been). We
+only ask that proper credit be given to the authors. 
+
+Like all software, it is copyrighted. It is not trademarked, but we do
+ask the following: 
+
+If you modify the source for these routines we ask that you change the
+name of the routine and comment the changes made to the original. 
+
+We will gladly answer any questions regarding the software. If a
+modification is done, however, it is the responsibility of the person
+who modified the routine to provide support. 

atlas-lapack/lapack.patch

@@ -0,0 +1,20 @@
+--- SRC/Makefile.old	2011-02-08 17:39:23.966666767 +0100
++++ SRC/Makefile	2011-02-08 17:40:52.990000016 +0100
+@@ -146,7 +146,7 @@
+    sgeequb.o ssyequb.o spoequb.o sgbequb.o \
+    sbbcsd.o slapmr.o sorbdb.o sorcsd.o
+ 
+-DSLASRC = spotrs.o sgetrs.o spotrf.o sgetrf.o 
++DSLASRC = spotrs.o sgetrs.o sgetrf.o 
+ 
+ SXLASRC = sgesvxx.o sgerfsx.o sla_gerfsx_extended.o sla_geamv.o		\
+    sla_gercond.o sla_rpvgrw.o ssysvxx.o ssyrfsx.o			\
+@@ -227,7 +227,7 @@
+    cla_hercond_c.o cla_hercond_x.o cla_herpvgrw.o \
+    cla_lin_berr.o clarscl2.o clascl2.o cla_wwaddw.o
+ 
+-ZCLASRC = cpotrs.o cgetrs.o cpotrf.o cgetrf.o 
++ZCLASRC = 
+ 
+ DLASRC = \
+    dgbbrd.o dgbcon.o dgbequ.o dgbrfs.o dgbsv.o  \

atlas-lapack/makefile.shared.mt

@@ -0,0 +1,23 @@
+include Make.inc
+
+all: libatlas.so libf77blas.so libcblas.so libblas.so liblapack.so.3.4.0
+
+
+libatlas.so: libatlas.a
+	ld $(LDFLAGS) -shared -soname $@ -o $@ --whole-archive libatlas.a \
+	   --no-whole-archive -lc $(LIBS)
+
+libf77blas.so : libptf77blas.a libatlas.so
+	ld $(LDFLAGS) -shared -soname libblas.so.3 -o $@ --whole-archive \
+	   libptf77blas.a --no-whole-archive $(F77SYSLIB) -L. -latlas
+
+libcblas.so : libptcblas.a libatlas.so
+	ld $(LDFLAGS) -shared -soname libcblas.so -o $@ --whole-archive \
+	   libptcblas.a -L. -latlas
+
+libblas.so: libf77blas.so
+	ln -s $< $@
+
+liblapack.so.3.4.0 : liblapack.a libcblas.so libblas.so
+	ld $(LDFLAGS) -shared -soname liblapack.so.3 -o $@ --whole-archive \
+	   liblapack.a --no-whole-archive $(F77SYSLIB) -L. -lcblas -lblas -lgcc_s

atlas-lapack/makefile.shared.st

@@ -0,0 +1,23 @@
+include Make.inc
+
+all: libatlas.so libf77blas.so libcblas.so libblas.so liblapack.so.3.4.0
+
+
+libatlas.so: libatlas.a
+	ld $(LDFLAGS) -shared -soname $@ -o $@ --whole-archive libatlas.a \
+	   --no-whole-archive -lc $(LIBS)
+
+libf77blas.so : libf77blas.a libatlas.so
+	ld $(LDFLAGS) -shared -soname libblas.so.3 -o $@ --whole-archive \
+	   libf77blas.a --no-whole-archive $(F77SYSLIB) -L. -latlas
+
+libcblas.so : libcblas.a libatlas.so
+	ld $(LDFLAGS) -shared -soname $@ -o $@ --whole-archive libcblas.a \
+	    -L. -latlas
+
+libblas.so: libf77blas.so
+	ln -s $< $@
+
+liblapack.so.3.4.0 : liblapack.a libcblas.so libblas.so
+	ld $(LDFLAGS) -shared -soname liblapack.so.3 -o $@ --whole-archive \
+	   liblapack.a --no-whole-archive $(F77SYSLIB) -L. -lcblas -lblas -lgcc_s

atlas-lapack/misdetects_i1_as_i2.patch

@@ -0,0 +1,13 @@
+--- CONFIG/src/backend/archinfo_x86.c.orig	2011-12-10 13:25:13.145469768 +0100
++++ CONFIG/src/backend/archinfo_x86.c	2011-12-10 13:26:23.358198406 +0100
+@@ -309,9 +309,9 @@
+       case 0x1A:
+       case 0x1E:
+       case 0x1F:
++      case 0x25:
+          iret = IntCorei1;
+          break;
+-      case 0x25:
+       case 0x2A:
+          iret = IntCorei2;
+ 	 break;

sage-mathematics/PKGBUILD

@@ -1,96 +1,115 @@
 #
 # Platform Packages for Chakra, part of chakra-project.org
 #
-# maintainer (i686): Phil Miller <philm[at]chakra-project[dog]org>
+# maintainer: Manuel Tortosa <manutortosa[at]chakra-project[dot]org>
-# maintainer (x86_64): Manuel Tortosa <manutortosa[at]chakra-project[dot]org>
-
-# include global config
-source ../_buildscripts/${current_repo}-${_arch}-cfg.conf
 
 pkgname=sage-mathematics
-pkgver=4.7
+pkgver=4.8
 pkgrel=1
-pkgdesc='SAGE: Open Source Mathematics Software, a viable free alternative to Magma, Maple, Mathematica, and Matlab.'
+pkgdesc='Open Source Mathematics Software, a viable free alternative to Magma, Maple, Mathematica, and Matlab.'
 url='http://www.sagemath.org'
 arch=('i686' 'x86_64')
 license=('GPL')
-depends=('ppl')
+depends=('atlas-lapack')
-makedepends=('gcc-fortran' 'gcc-libs' 'desktop-file-utils' 'imagemagick' 'texlive-core')
+makedepends=('gcc-fortran' 'desktop-file-utils' 'texlive-core')
-optdepends=('imagemagick: some plotting functionality benefits from it'
+optdepends=('ffmpeg: to show animations' 'imagemagick: to show animations and some LaTeX output in the notebook'
-            'texlive-core: some plotting functionality benefits from it')
+            'texlive-core: to view LaTeX output in the notebook and to use SageTeX'
-options=('!makeflags')
+            'jsmath-fonts: native TeX fonts for the notebook'
-install="${pkgname}.install"
+            'openssh: to use the notebook in secure mode')
-source=("http://sage.math.washington.edu/home/release/sage-${pkgver}/sage-${pkgver}.tar"
+install="$pkgname.install"
-        'SAGE-notebook.desktop')
+source=("http://boxen.math.washington.edu/home/release/sage-$pkgver/sage-$pkgver.tar"
-md5sums=('db4d891feed487e1696b8d01ae3b6469'
+  "http://boxen.math.washington.edu/home/leif/Sage/spkgs/gfan-0.4plus.p3.spkg"
-         'dc391f12b7d17dd37326343ec0e99bbd')
+  "http://boxen.math.washington.edu/home/leif/Sage/spkgs/givaro-3.2.13.rc1.p4.spkg"
+  'SAGE-notebook.desktop' 'polybori_gcc47.patch')
+noextract=("gfan-0.4plus.p3.spkg" "givaro-3.2.13.rc1.p4.spkg")
+md5sums=('3e9725846a20f624a9a6811107fc5cb0'
+         '2e35abd57788571faf6b638802bff470'
+         'a84996518e39a1197eaf63562d8fe734'
+         'cc47a29bc32fbdea48f8a19e2ad70441'
+         '21462df65ca8bc72988022ba572a0753')
+
 
 build() {
-  cd sage-${pkgver}
+  cd sage-$pkgver
 
-  # modularization of sage, sort of :)
+  # fix gfan build with GCC 4.7 http://trac.sagemath.org/sage_trac/ticket/12760
-  #mkdir -p spkg/installed
+  mv ../gfan-0.4plus.p3.spkg spkg/standard
-  #touch spkg/installed/readline-6.1
+  rm spkg/standard/gfan-0.4plus.p1.spkg 
-  mkdir -p spkg/installed
+
-  touch spkg/installed/ppl-0.11.2
+  # fix sage library build with GCC 4.7 http://trac.sagemath.org/sage_trac/ticket/12760
+  mv ../givaro-3.2.13.rc1.p4.spkg spkg/standard
+  rm spkg/standard/givaro-3.2.13.rc1.p3.spkg
+
+  # fix polybori build with GCC 4.7 http://trac.sagemath.org/sage_trac/ticket/12750
+  cd spkg/standard
+  tar xjf polybori-0.7.1.p6.spkg
+  patch -p0 -i $srcdir/polybori_gcc47.patch
+  tar cjf polybori-0.7.1.p6.spkg polybori-0.7.1.p6
+  rm -r polybori-0.7.1.p6
+  cd ../..
+    
+  # fix missing symbol _ZN23Parma_Polyhedra_Library13have_sse_unitE on i686 http://trac.sagemath.org/sage_trac/ticket/11391
+  if [[ "$CARCH" == "i686" ]]; then
+   cd spkg/standard
+   tar xjf ppl-0.11.2.p0.spkg
+   sed -i 's/--enable-interfaces=c++/--enable-interfaces="c++ c"/' ppl-0.11.2.p0/spkg-install
+   tar cjf ppl-0.11.2.p0.spkg ppl-0.11.2.p0
+   rm -r ppl-0.11.2.p0
+   cd ../..
+  fi
 
-  # fix "missing sage.all error" during build
   unset CFLAGS
   unset CXXFLAGS
-
-  # fix build errors
   unset LDFLAGS
 
-  # enable multiple threads while building, is this really needed? check if uses MAKEFLAGS
+  # fix polybori, linbox and sage library build with GCC 4.7 http://trac.sagemath.org/sage_trac/ticket/12751
-  export SAGE_BUILD_THREADS=$(lscpu | awk '/^CPU\(s\):/ { print $2 }')
+  export CXX="g++ -fpermissive"
-  export MAKE="make -j${SAGE_BUILD_THREADS}"
 
-  # use Chakra's fortran rather then the one that ships with sage to compile sage's fortran
+  # parallel build
+  export MAKE="make -j2"
+
+  # use archlinux's fortran
   export SAGE_FORTRAN='/usr/bin/gfortran'
   export SAGE_FORTRAN_LIB='/usr/lib/libgfortran.so'
 
+  # use external ATLAS
+  [[ $USE_EXTERNAL_ATLAS ]] && export SAGE_ATLAS_LIB='/usr/lib'
+
   # disable building with debugging support
   export SAGE_DEBUG='no'
 
   # enable fat binaries (disables processor specific optimizations)
   # comment out if you're only building it for yourself
-  export SAGE_FAT_BINARY='yes'
+  # export SAGE_FAT_BINARY='yes'
-
+  
-  # can't write to root in a clean chroot
-  export DOT_SAGE='/build/src/'
-
-  # only build sage, no documents
-  #make build
   make
+}
 
-  # uncomment if we want to run all the tests (warning: very long)
+check() {
-  #make ptestlong
+  cd sage-$pkgver
+
+  make ptest || /bin/true
+
+  # uncomment if you want to run all the tests (warning: very long)
+  # make ptestlong || /bin/true
 }
 
 package() {
-  cd sage-${pkgver}
+  cd sage-$pkgver
 
   # cp because make install is experimental and will corrupt the install
-  install -d ${pkgdir}/opt/sage
+  install -d $pkgdir/opt/sage
-  cp -r * ${pkgdir}/opt/sage
+  cp -r * $pkgdir/opt/sage
 
-  # move SageTeX files to more appropriate directory
+  desktop-file-install $srcdir/SAGE-notebook.desktop --dir $pkgdir/usr/share/applications 
-  install -d ${pkgdir}/usr/share
-  mv ${pkgdir}/opt/sage/local/share/texmf \
-    ${pkgdir}/usr/share
-
-  desktop-file-install ${srcdir}/SAGE-notebook.desktop \
-    --dir ${pkgdir}/usr/share/applications 
 
   # create link to main binary
-  install -d ${pkgdir}/usr/bin
+  install -d $pkgdir/usr/bin
-  ln -s /opt/sage/sage ${pkgdir}/usr/bin/sage
+  ln -s /opt/sage/sage $pkgdir/usr/bin/sage
 
   # remove build logs
-  rm -f ${pkgdir}/opt/sage/install.log
+  rm -f $pkgdir/opt/sage/install.log
-  rm -rf ${pkgdir}/opt/sage/spkg/logs
 
-  # remove source packages, since they are rarely needed, they are 300mb in size (compressed), and no need to compile them, put them into aur/sage-mathematics-spkgs
+  # remove source packages
-  rm -f ${pkgdir}/opt/sage/spkg/base/*spkg
+  rm -rf $pkgdir/opt/sage/spkg/{base,standard,logs}
-  rm -f ${pkgdir}/opt/sage/spkg/standard/*spkg
 }

sage-mathematics/SAGE-notebook.desktop

@@ -1,8 +1,8 @@
 [Desktop Entry]
 Version=1.0
 Name=SAGE
-Comment=SAGE NOTEBOOK
+Comment=SAGE notebook
-Comment[en_US]=SAGE NOTEBOOK
+Comment[en_US]=SAGE notebook
 Exec=/opt/sage/sage -notebook
 GenericName=
 GenericName[de]=
@@ -12,7 +12,7 @@ Name[de]=SAGE
 StartupNotify=true
 Terminal=true
 Type=Application
-Categories=Science;Math;
+Categories=Education;Science;Math;
 X-DCOP-ServiceType=
 X-KDE-SubstituteUID=false
 X-KDE-Username=

sage-mathematics/polybori_gcc47.patch

@@ -0,0 +1,19 @@
+# HG changeset patch
+# User Alexander Dreyer <adreyer@gmx.de>
+# Date 1332364717 -3600
+# Node ID 43b3931ceed7b57c4c5385442de6ff45bd0f477c
+# Parent  617ce1a715329d16e5ebde0bfdde9c4d09072451
+FIX explict name lookups (in template base)
+
+diff -r 617ce1a715329d16e5ebde0bfdde9c4d09072451 -r 43b3931ceed7b57c4c5385442de6ff45bd0f477c libpolybori/include/polybori/orderings/CBlockOrderingFacade.h
+--- polybori-0.7.1.p6/src/polybori-0.7/polybori/include/CBlockOrderingFacade.h	Mon Mar 19 22:53:46 2012 +0100
++++ polybori-0.7.1.p6/src/polybori-0.7/polybori/include/CBlockOrderingFacade.h	Wed Mar 21 22:18:37 2012 +0100
+@@ -91,7 +91,7 @@
+     CacheManager<order_lead_tag> cache_mgr(poly.ring());
+     typename base_type::descending_property descending;
+ 
+-    return monom(  dd_block_degree_lead(cache_mgr, blockDegCache, 
++    return base_type::monom( dd_block_degree_lead(cache_mgr, blockDegCache, 
+                                         poly.navigation(), m_indices.begin(),
+                                         set_type(poly.ring()), descending) );
+   }