Merge branch 'develop' into t/20382/replace_is_package_installed_with…

…_features

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.2.beta2, Release Date: 2016-04-01
+SageMath version 7.2.beta3, Release Date: 2016-04-07

build/pkgs/cddlib/spkg-install

@@ -28,7 +28,7 @@ cd src
 cp ../patches/random.{c,h} lib-src/
 cp ../patches/random.{c,h} lib-src-gmp/
 
-# Required by sage.geometry.polyhedra 
+# Required by sage.geometry.polyhedron
 cp ../patches/cdd_both_reps.c src/
 cp ../patches/cdd_both_reps.c src-gmp/cdd_both_reps.c
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8cf7b09fdc4d8326d489ead1b1b83b5dc58c872c
-md5=e6a347567b1ea00823f489bfc6afa196
-cksum=3730099068
+sha1=00d7bd6cb4d1cb6ef378cf2ecc0bfe733abf845e
+md5=36b19a7d55b3a105f7971b3380a22baf
+cksum=1610953959

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-156
+157

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=ee455e4f6bedb8d02325da1d4810ab906c3ddc1d
-md5=66b62989a67c55af016c916da36e7514
-cksum=3621634163
+sha1=32f12b8dd976111668ef8ba7e716a850869a0bf6
+md5=14fbc970f4a856845e633cbc09e61048
+cksum=2292891014

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.23.5
+0.24.p0

build/pkgs/gap3/SPKG.txt

@@ -0,0 +1,73 @@
+= Jean Michel's GAP 3 distribution =
+
+== Description ==
+
+This package installs Jean Michel's pre-packaged GAP3, which is a minimal GAP3
+distribution containing packages that have no equivalent in GAP4.
+
+Below is the full description from Jean Michel's webpage
+(accessed 23 July 2015).
+
+    A pre-packaged GAP3 with everything you need
+
+    To help people who are just interested in GAP3 because they need a package
+    which has not been ported to GAP4, I have prepared an easy-to install
+    minimal GAP3 distribution containing an up-to-date versions of the
+    packages:
+
+        anusq, arep, autag, chevie, cryst, dce, grim, matrix, meataxe, monoid,
+        nq, pcqa, sisyphos, specht, ve, vkcurve.
+
+    These packages have been chosen since most have no equivalent in GAP4. They
+    are autoloaded when starting gap.
+
+    This distribution includes only partial lists of small groups, 2-groups,
+    3-groups, character tables from the Atlas and tables of marks. It does not
+    include either the packages:
+
+        anupq, grape, kbmag, xgap, cohomolo, gliss, guava, xmod
+
+    which have some equivalent in GAP4. You can get these extra features at
+
+        http://www.math.rwth-aachen.de/~Frank.Luebeck/gap/GAP3
+
+    In this distribution:
+
+    - The on-line help includes the documentation of the included packages.
+    - The html documentation (htm/index.html) also does.
+    - The manual (manual.pdf) also does.
+
+== License ==
+
+Most parts of the GAP distribution, including the core part of the GAP system,
+are distributed under the terms of the GNU General Public License (see
+http://www.gnu.org/licenses/gpl.html or the file GPL in the etc directory of
+the GAP installation).
+
+== SPKG Maintainers ==
+
+* Christian Stump <christian.stump@gmail.com>
+
+== Upstream Contact ==
+
+Jean Michel <jmichel@math.jussieu.fr>
+http://webusers.imj-prg.fr/~jean.michel/
+
+== Special Update/Build Instructions ==
+
+The difference between the distributed tarball and Jean Michel's
+original tarball is that all binary files have been deleted one by one
+from the listing obtained by
+
+    grep -r -m 1 "^"  . | grep "^Binary file"
+
+=== Patches ===
+
+ * gap3_makefile.patch: modifies src/src/Makefile such that if autodetects
+   the system
+
+ * gap3_startup.patch: modifies src/bin/gap.sh to set GAP_DIR and GAP_PRG
+
+== Dependencies ===
+
+None

build/pkgs/gap3/checksums.ini

@@ -0,0 +1,4 @@
+tarball=gap3-VERSION.tar.gz
+sha1=0d64737250f3e028716881c9d7e82338c80244d0
+md5=569bf72d516c1da183d43f09851fa1bb
+cksum=3760972699

build/pkgs/gap3/dependencies

@@ -0,0 +1 @@
+# no dependencies

build/pkgs/gap3/package-version.txt

@@ -0,0 +1 @@
+jm5-2015-02-01

build/pkgs/gap3/patches/gap3_init.patch

@@ -0,0 +1,33 @@
+Commenting out the optional packages
+RequirePackage("arep");
+RequirePackage("meataxe");
+RequirePackage("nq");
+RequirePackage("sisyphos");
+RequirePackage("ve");
+
+diff -ur src/gap3/lib/init.g.orig src/gap3/lib/init.g
+--- src/gap3/lib/init.g.orig	2016-03-30 17:58:09.557517250 +0200
++++ src/gap3/lib/init.g	2016-03-30 17:58:23.265517363 +0200
+@@ -1142,17 +1142,17 @@
+ Print(" gap3-jm5 final 21Mar2016 -- see webusers.imj-prg.fr/~jmichel/gap3\n");
+ Print(" Minimal distribution -- loading the following packages:\n");
+ fi;
+-RequirePackage("anusq");
++#RequirePackage("anusq");
+ RequirePackage("arep");
+ RequirePackage("autag");
+ RequirePackage("cryst");
+ RequirePackage("dce");
+ RequirePackage("grim");
+ RequirePackage("matrix");
+-RequirePackage("meataxe");
++#RequirePackage("meataxe");
+ RequirePackage("monoid");
+-RequirePackage("nq");
++#RequirePackage("nq");
+ RequirePackage("pcqa");
+-RequirePackage("sisyphos");
+-RequirePackage("ve");
++#RequirePackage("sisyphos");
++#RequirePackage("ve");
+ RequirePackage("chevie"); # requires vkcurve, specht, algebra

build/pkgs/gap3/patches/gap3_makefile.patch

@@ -0,0 +1,153 @@
+Adding the option to autodetect the system and running "make" without
+any options specifying the system.
+
+diff -ur src/gap3/src/Makefile.orig src/gap3/src/Makefile
+--- src/gap3/src/Makefile.orig     2016-03-24 11:35:24.027893512 +0100
++++ src/gap3/src/Makefile  2016-03-24 11:35:07.515893376 +0100
+@@ -48,6 +48,9 @@
+ ##  DJGPP differently you have to change this below.
+ ##
+ #H  $Log: Makefile,v $
++#H  Revision 2016/03/11 Christian Stump
++#H  Autouse Linux/Darvin and 32bit/64bit.
++#H
+ #H  Revision 2014/08/22 Jean Michel
+ #H  remove obsolete targets. Add 64bit target.
+ #H
+@@ -105,103 +108,40 @@
+ ##
+ SHELL = /bin/sh
+
+-#############################################################################
+-##
+-#T  Targets . . . . .  targets of the form <vendor>-<cpu>-<system>-<compiler>
+-##
+-##  Following are the targets that the	user can specify.  Each target	calls
+-##  'make' recursively twice.
+-##
+-##  The first time it calls
+-##
+-##	@$(MAKE) <system-file>.o  CFLAGS="$(COPTS) <copts>"
+-##
+-##  where <system-file> is either 'system' or the name of another system file
+-##  and where <copts> are the options to  pass to  pass	 to  the  C compiler,
+-##  e.g., 'SYS_IS_BSD' or 'SYS_IS_MSDOS'.
+-##
+-##  The second time it calls
+-##
+-##	@$(MAKE) gap  CC=<c-compiler> CFLAGS="$(COPTS) <opts>" \
+-##		      SYS_FILE=<system-file>.o LOPTS="$(LOPTS)"
+-##
+-##  where <system-file> is the same file as above, <c-compiler> is  the	 name
+-##  of the C compiler to use ($(CC) is used if this is not present),  <copts>
+-##  are	 the options to pass ot	 the  C compiler, e.g., '-O2'.
+-##
+-unknown:
+-	@echo "usage: 'make <target>' where target is one of"
+-	@echo "'x86linux-gcc64'   for x86linux with gcc"
+-	@echo "'x86linux-gcc'     for x86linux with gcc in 32bit mode"
+-	@echo "'macosx-gcc'       for mac os x with gcc"
+-	@echo "'x86bsd-gcc'       for x86BSD with gcc"
+-	@echo "'sun-sparc-solaris-gcc' for SUN under Solaris with GNU cc"
+-	@echo "'sun-sparc-solaris-cc'  for SUN under Solaris with cc"
+-	@echo "'bsd'		       for others under Berkeley UNIX with cc"
+-	@echo "	"
+-	@echo "	  additional C compiler and linker flags can be passed with"
+-	@echo "	  'make <target> COPTS=<compiler-opts> LOPTS=<linker-opts>',"
+-	@echo "	  i.e., 'make x86linux-gcc COPTS=-g LOPTS=-g for debug'"
+-
+-x86linux-gcc:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -m32 -O2 -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO -DSYS_HAS_IOCTL_PROTO"
+-	@$(MAKE) gap CC=gcc CFLAGS="$(COPTS) -m32 -O " SYS_FILE=system.o LOPTS="$(LOPTS) -m32 -static"
+-	strip gap
+-	mv gap ../bin/gap.x86linux
+-
+-x86linux-gccd:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="-g -m32 -O2 -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO -DSYS_HAS_IOCTL_PROTO"
+-	@$(MAKE) gap CC=gcc CFLAGS="-g -m32 -O " SYS_FILE=system.o LOPTS="-g -m32 -static"
+-
+-x86linux-gcc64:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -O -DSYS_IS_64_BIT -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO -DSYS_HAS_IOCTL_PROTO"
+-	@$(MAKE) gap CC=gcc CFLAGS="$(COPTS) -O -DSYS_IS_64_BIT " SYS_FILE=system.o LOPTS="$(LOPTS) -static"
+-	strip gap
+-	mv gap ../bin/gap.x86linux64
+-
+-x86-dos-djgpp:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -DSYS_IS_MSDOS_DJGPP -DSYS_HAS_MISC_PROTO"
+-	@$(MAKE) gapdjg.exe CC=gcc  CFLAGS="$(COPTS) -O1"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
+-
+-x86-dos-djgppcross:
+-	@$(MAKE) system.o   CC=dos-gcc	CFLAGS="$(COPTS) -DSYS_IS_MSDOS_DJGPP -DSYS_HAS_MISC_PROTO"
+-	@$(MAKE) gapdjg.exe CC=dos-gcc	CFLAGS="$(COPTS) -O1"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
+-
+-# sbrk doesn't work in macosx so we need to use vm_allocate
+-macosx-gcc:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -m32 -DSYS_IS_MACOSX -DARCH_INCLUDE -DSYS_HAS_IOCTL_PROTO"
+-	@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS) -m32 -O2"  SYS_FILE=system.o  LOPTS="$(LOPTS) -m32"
++ARCH = $(shell getconf LONG_BIT)
++UNAME_S = $(shell uname -s)
+
+-# sbrk doesn't work in macosx so we need to use vm_allocate
+-# This is using Frank Luebeck's optimized compile....but it doesn't
+-# change the GAPstones for the files in ../tst
+-macosx-gcc-686-optimized:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -m32 -fomit-frame-pointer -pipe -fno-strength-reduce -march=i686 -falign-loops=2 -falign-jumps=2 -falign-functions=2 -DCPU=686 -g -O2 -DSYS_IS_MACOSX -DARCH_INCLUDE -DSYS_HAS_IOCTL_PROTO"
+-	@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS) -m32 -fomit-frame-pointer -pipe -fno-strength-reduce -march=i686 -falign-loops=2 -falign-jumps=2 -falign-functions=2 -DCPU=686 -g -O3"  SYS_FILE=system.o  LOPTS="$(LOPTS) -m32"
+-
+-sun-sparc-solaris-cc:
+-	@$(MAKE) system.o   CC=cc  CFLAGS="$(COPTS) -O -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSOLARIS2"
+-	@echo "Don't worry about 'out of range' and 'overflow' warnings"
+-	@echo "(29 in total)"
+-	@$(MAKE) gap	    CC=cc  CFLAGS="$(COPTS) -O2"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
+-
+-sun-sparc-solaris-gcc2:						   
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS)  -O6 -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSOLARIS2"						       
+-	@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS)  -O6"  SYS_FILE=system.o LOPTS="$(LOPTS)"								     
+-
+-# 'sys/times.h' claims 'times' returns 'clock_t' (how shall it return -1?)
+-sun-sparc-sunos-gcc:
+-	@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO"
+-	@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS) -O2"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
+-
+-# 'sys/times.h' claims 'times' returns 'clock_t' (how shall it return -1?)
+-sun-sparc-sunos-cc:
+-	@$(MAKE) system.o   CFLAGS="$(COPTS) -DSYS_IS_USG -DSYS_HAS_TIME_PROTO"
+-	@$(MAKE) gap	    CFLAGS="$(COPTS) -O"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
+-
+-bsd:
+-	@$(MAKE) system.o   CC=$(CC)  CFLAGS="$(COPTS) -DSYS_IS_BSD"
+-	@$(MAKE) gap	    CC=$(CC)  CFLAGS="$(COPTS) -O"  SYS_FILE=system.o  LOPTS="$(LOPTS)"
++unknown:
++	@echo "###########################################################"
++	@echo "#  Building GAP3 for '$(UNAME_S)' and '$(ARCH) bit'"
++	@echo "###########################################################"
++
++ifeq ($(UNAME_S),Linux)
++    ifeq ($(ARCH),64)
++		@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -O -DSYS_IS_64_BIT -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO -DSYS_HAS_IOCTL_PROTO"
++		@$(MAKE) gap CC=gcc CFLAGS="$(COPTS) -O -DSYS_IS_64_BIT " SYS_FILE=system.o LOPTS="$(LOPTS) -static"
++		mv gap ../bin/gap3
++    else
++		@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -O2 -DSYS_IS_USG -DSYS_HAS_TIME_PROTO -DSYS_HAS_SIGNAL_PROTO -DSYS_HAS_IOCTL_PROTO"
++		@$(MAKE) gap CC=gcc CFLAGS="$(COPTS) -O " SYS_FILE=system.o LOPTS="$(LOPTS) -static"
++		mv gap ../bin/gap3
++    endif
++endif
++ifeq ($(UNAME_S),Darwin)
++    ifeq ($(ARCH),64)
++		@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -DSYS_IS_MACOSX -DSYS_IS_64_BIT -DARCH_INCLUDE -DSYS_HAS_IOCTL_PROTO"
++		@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS) -O2 -DSYS_IS_MACOSX -DSYS_IS_64_BIT "  SYS_FILE=system.o  LOPTS="$(LOPTS)"
++		mv gap ../bin/gap3
++    else
++		@$(MAKE) system.o   CC=gcc  CFLAGS="$(COPTS) -DSYS_IS_MACOSX -DARCH_INCLUDE -DSYS_HAS_IOCTL_PROTO"
++		@$(MAKE) gap	    CC=gcc  CFLAGS="$(COPTS) -O2 -DSYS_IS_MACOSX "  SYS_FILE=system.o  LOPTS="$(LOPTS)"
++		mv gap ../bin/gap3
++    endif
++endif
++
++	@echo "###########################################################"
++	@echo "#  Building complete, you can run GAP3 from './../bin/gap3'"
++	@echo "###########################################################"
+
+ #############################################################################
+ ##