Merge branch 'develop' into public/combinat/rigged_configurations/met…

…hods-15560

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta1, released 2014-05-13
+Sage version 6.3.beta2, released 2014-05-24

build/deps

@@ -158,12 +158,12 @@ $(INST)/prereq: ../configure
 	        echo "If you would like to try to build Sage anyway (to help porting),"; \
 	        echo "export the variable 'SAGE_PORT' to something non-empty."; \
 	        exit 1; \
-    	else \
+	    else \
 	        echo "Since 'SAGE_PORT' is set, we will try to build anyway."; \
-    	fi; )
+	    fi; )
 	touch $@
 
-$(INST)/$(BZIP2): $(INST)/prereq
+$(INST)/$(BZIP2): $(INST)/prereq $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
 $(INST)/$(PATCH): $(INST)/$(BZIP2)
@@ -176,7 +176,7 @@ $(INST)/$(PATCH): $(INST)/$(BZIP2)
 $(INST)/$(ATLAS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(ATLAS) 2>&1" "tee -a $(SAGE_LOGS)/$(ATLAS).log"
 
-$(INST)/$(BOEHM_GC):
+$(INST)/$(BOEHM_GC): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BOEHM_GC) 2>&1" "tee -a $(SAGE_LOGS)/$(BOEHM_GC).log"
 
 $(INST)/$(BOOST_CROPPED):
@@ -185,7 +185,7 @@ $(INST)/$(BOOST_CROPPED):
 $(INST)/$(CLIQUER):
 	+$(PIPE) "$(SAGE_SPKG) $(CLIQUER) 2>&1" "tee -a $(SAGE_LOGS)/$(CLIQUER).log"
 
-$(INST)/$(NCURSES):
+$(INST)/$(NCURSES): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NCURSES) 2>&1" "tee -a $(SAGE_LOGS)/$(NCURSES).log"
 
 $(INST)/$(READLINE): $(INST)/$(NCURSES)
@@ -211,7 +211,7 @@ $(INST)/$(GRAPHS):
 $(INST)/$(GLPK): $(INST)/$(MPIR) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(GLPK) 2>&1" "tee -a $(SAGE_LOGS)/$(GLPK).log"
 
-$(INST)/$(PYTHON): $(INST)/$(ZLIB) $(INST)/$(BZIP2) \
+$(INST)/$(PYTHON): $(INST)/$(ZLIB) $(INST)/$(BZIP2) $(INST)/$(PKGCONF) \
 		   $(INST)/$(READLINE) $(INST)/$(SQLITE) $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(PYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(PYTHON).log"
 
@@ -401,7 +401,7 @@ $(INST)/$(ECL): $(INST)/$(MPIR) $(INST)/$(READLINE) $(INST)/$(BOEHM_GC)
 $(INST)/$(MAXIMA): $(INST)/$(ECL)
 	+$(PIPE) "$(SAGE_SPKG) $(MAXIMA) 2>&1" "tee -a $(SAGE_LOGS)/$(MAXIMA).log"
 
-$(INST)/$(R): $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(READLINE)
+$(INST)/$(R): $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(READLINE) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(R) 2>&1" "tee -a $(SAGE_LOGS)/$(R).log"
 
 $(INST)/$(RPY): $(INST)/$(PYTHON) $(INST)/$(R)
@@ -422,7 +422,7 @@ $(INST)/$(FLINT): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(NTL)
 $(INST)/$(ECLIB): $(INST)/$(PARI) $(INST)/$(NTL) $(INST)/$(FLINT)
 	+$(PIPE) "$(SAGE_SPKG) $(ECLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(ECLIB).log"
 
-$(INST)/$(M4RI): $(INST)/$(LIBPNG)
+$(INST)/$(M4RI): $(INST)/$(LIBPNG) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(M4RI) 2>&1" "tee -a $(SAGE_LOGS)/$(M4RI).log"
 
 $(INST)/$(M4RIE): $(INST)/$(M4RI) $(INST)/$(GIVARO) $(INST)/$(NTL)
@@ -527,7 +527,7 @@ $(INST)/$(PKGCONF):
 $(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
 
-$(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
+$(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
 
 $(INST)/$(SCIPY): $(INST)/$(ATLAS) $(INST)/$(NUMPY)

build/pkgs/atlas/spkg-install

@@ -329,7 +329,7 @@ def configure(arch=None, isa_ext=None):
 
     # use hard floats on ARM
     if conf['ARM?']:
-        cmd += '-D c -DATL_ARM_HARDFP=1'
+        cmd += ' -D c -DATL_ARM_HARDFP=1'
 
     # set machine architecture
     if arch is not None:

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.am.patch

@@ -12,3 +12,10 @@ index b3ab11a..a9673b8 100644
 
  include_HEADERS = \
  cdd.h \
+@@ -24,5 +25,5 @@
+ cddtypes_f.h \
+ setoper.h
+
+-AM_CPPFLAGS = -I$(gmpincludedir) -DGMPRATIONAL
++AM_CPPFLAGS = -DGMPRATIONAL
+ AM_LDFLAGS = -version-info 0:0:0

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.in.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/lib-src-gmp/Makefile.in b/src/lib-src-gmp/Makefile.in
 index 4ab9342..93ff335 100644
 --- a/src.bak/lib-src-gmp/Makefile.in
 +++ b/src/lib-src-gmp/Makefile.in
-@@ -54,7 +54,7 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
+@@ -54,7 +54,7 @@
  libcddgmp_la_LIBADD =
  am_libcddgmp_la_OBJECTS = cddcore.lo cddlp.lo cddmp.lo cddio.lo \
  	cddlib.lo cddproj.lo cddcore_f.lo cddlp_f.lo cddmp_f.lo \
@@ -11,7 +11,7 @@ index 4ab9342..93ff335 100644
  libcddgmp_la_OBJECTS = $(am_libcddgmp_la_OBJECTS)
  DEFAULT_INCLUDES = -I.@am__isrc@
  depcomp = $(SHELL) $(top_srcdir)/depcomp
-@@ -199,7 +199,8 @@ cddmp_f.c \
+@@ -199,7 +199,8 @@
  cddio_f.c \
  cddlib_f.c \
  cddproj_f.c \
@@ -21,7 +21,16 @@ index 4ab9342..93ff335 100644
 
  include_HEADERS = \
  cdd.h \
-@@ -293,6 +294,7 @@ distclean-compile:
+@@ -210,7 +211,7 @@
+ cddtypes_f.h \
+ setoper.h
+
+-AM_CPPFLAGS = -I$(gmpincludedir) -DGMPRATIONAL
++AM_CPPFLAGS = -DGMPRATIONAL
+ AM_LDFLAGS = -version-info 0:0:0
+ all: all-am
+
+@@ -293,6 +294,7 @@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddmp_f.Plo@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddproj.Plo@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddproj_f.Plo@am__quote@

build/pkgs/cddlib/patches/src-gmp_Makefile.am.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/src-gmp/Makefile.am b/src/src-gmp/Makefile.am
 index e4dbb86..e579d71 100644
 --- a/src.bak/src-gmp/Makefile.am
 +++ b/src/src-gmp/Makefile.am
-@@ -11,7 +11,8 @@ testcdd1_gmp \
+@@ -11,7 +11,8 @@
  testcdd2_gmp \
  testlp1_gmp \
  testlp2_gmp \
@@ -12,11 +12,15 @@ index e4dbb86..e579d71 100644
  #cddmathlink
 
  scdd_gmp_SOURCES                   = simplecdd.c
-@@ -27,6 +28,7 @@ testcdd2_gmp_SOURCES               = testcdd2.c
+@@ -27,10 +28,9 @@
  testlp1_gmp_SOURCES                = testlp1.c
  testlp2_gmp_SOURCES                = testlp2.c
  testlp3_gmp_SOURCES                = testlp3.c
 +cdd_both_reps_gmp_SOURCES          = cdd_both_reps.c
  # cddmathlink_SOURCES                = cddmathlink.c cddmlio.h cddmlio.c
 
  LDADD        = ../lib-src-gmp/libcddgmp.la
+-AM_LDFLAGS   = -L$(gmplibdir)
+ INCLUDES     = -I../lib-src-gmp
+-INCLUDES    += -I$(gmpincludedir)
+ AM_CPPFLAGS  = -DGMPRATIONAL

build/pkgs/cddlib/patches/src-gmp_Makefile.in.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/src-gmp/Makefile.in b/src/src-gmp/Makefile.in
 index f88c83f..3470dc9 100644
 --- a/src.bak/src-gmp/Makefile.in
 +++ b/src/src-gmp/Makefile.in
-@@ -37,7 +37,8 @@ bin_PROGRAMS = scdd_gmp$(EXEEXT) lcdd_gmp$(EXEEXT) \
+@@ -37,7 +37,8 @@
  	projection_gmp$(EXEEXT) adjacency_gmp$(EXEEXT) \
  	allfaces_gmp$(EXEEXT) testshoot_gmp$(EXEEXT) \
  	testcdd1_gmp$(EXEEXT) testcdd2_gmp$(EXEEXT) \
@@ -12,7 +12,7 @@ index f88c83f..3470dc9 100644
  subdir = src-gmp
  DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
  ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-@@ -57,6 +58,10 @@ am_allfaces_gmp_OBJECTS = allfaces.$(OBJEXT)
+@@ -57,6 +58,10 @@
  allfaces_gmp_OBJECTS = $(am_allfaces_gmp_OBJECTS)
  allfaces_gmp_LDADD = $(LDADD)
  allfaces_gmp_DEPENDENCIES = ../lib-src-gmp/libcddgmp.la
@@ -23,7 +23,7 @@ index f88c83f..3470dc9 100644
  am_fourier_gmp_OBJECTS = fourier.$(OBJEXT)
  fourier_gmp_OBJECTS = $(am_fourier_gmp_OBJECTS)
  fourier_gmp_LDADD = $(LDADD)
-@@ -114,19 +119,19 @@ LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+@@ -114,19 +119,19 @@
  	--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
  	$(LDFLAGS) -o $@
  SOURCES = $(adjacency_gmp_SOURCES) $(allfaces_gmp_SOURCES) \
@@ -55,15 +55,20 @@ index f88c83f..3470dc9 100644
  ETAGS = etags
  CTAGS = ctags
  DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-@@ -254,6 +259,7 @@ testcdd2_gmp_SOURCES = testcdd2.c
+@@ -254,10 +259,10 @@
  testlp1_gmp_SOURCES = testlp1.c
  testlp2_gmp_SOURCES = testlp2.c
  testlp3_gmp_SOURCES = testlp3.c
 +cdd_both_reps_gmp_SOURCES = cdd_both_reps.c
  # cddmathlink_SOURCES                = cddmathlink.c cddmlio.h cddmlio.c
  LDADD = ../lib-src-gmp/libcddgmp.la
- AM_LDFLAGS = -L$(gmplibdir)
-@@ -326,6 +332,9 @@ adjacency_gmp$(EXEEXT): $(adjacency_gmp_OBJECTS) $(adjacency_gmp_DEPENDENCIES)
+-AM_LDFLAGS = -L$(gmplibdir)
+-INCLUDES = -I../lib-src-gmp -I$(gmpincludedir)
++INCLUDES = -I../lib-src-gmp
+ AM_CPPFLAGS = -DGMPRATIONAL
+ all: all-am
+
+@@ -326,6 +331,9 @@
  allfaces_gmp$(EXEEXT): $(allfaces_gmp_OBJECTS) $(allfaces_gmp_DEPENDENCIES) 
  	@rm -f allfaces_gmp$(EXEEXT)
  	$(LINK) $(allfaces_gmp_OBJECTS) $(allfaces_gmp_LDADD) $(LIBS)
@@ -73,7 +78,7 @@ index f88c83f..3470dc9 100644
  fourier_gmp$(EXEEXT): $(fourier_gmp_OBJECTS) $(fourier_gmp_DEPENDENCIES) 
  	@rm -f fourier_gmp$(EXEEXT)
  	$(LINK) $(fourier_gmp_OBJECTS) $(fourier_gmp_LDADD) $(LIBS)
-@@ -368,6 +377,7 @@ distclean-compile:
+@@ -368,6 +376,7 @@
 
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/adjacency.Po@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/allfaces.Po@am__quote@

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f53c1a13b8acb91f9c2841b2d1052a000ff447a3
-md5=1cbf074c0deb87f55cb638087009d1b7
-cksum=1973269113
+sha1=56399592db642ce25cd331edba8ceeecfa211393
+md5=030561c77e141c8e0c7c045b1c301964
+cksum=4180963490

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-29
+31

build/pkgs/ecl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ecl-VERSION.tar.bz2
-sha1=0f5a540bd6d089d206cce674e0c73f4036191547
-md5=204bb44496fdda0e552a987f003fed69
-cksum=1587965735
+sha1=c79fa3573afad1834cf6057c15f303505fc0011d
+md5=52ca39a0abd4d0822abdd9e909cc5ffd
+cksum=2846116483

build/pkgs/ecl/package-version.txt

@@ -1 +1 @@
-12.12.1.p4
+12.12.1.20140409

build/pkgs/ecl/patches/gmp.patch

@@ -0,0 +1,33 @@
+diff -druN src.orig/src/configure src/src/configure
+--- src.orig/src/configure	2012-12-07 22:01:02.000000000 +0100
++++ src/src/configure	2014-04-09 15:20:21.360905900 +0200
+@@ -2544,7 +2544,7 @@
+
+
+ ac_aux_dir=
+-for ac_dir in gmp "$srcdir"/gmp; do
++for ac_dir in . "$srcdir"/.; do
+   if test -f "$ac_dir/install-sh"; then
+     ac_aux_dir=$ac_dir
+     ac_install_sh="$ac_aux_dir/install-sh -c"
+@@ -2560,7 +2560,7 @@
+   fi
+ done
+ if test -z "$ac_aux_dir"; then
+-  as_fn_error $? "cannot find install-sh, install.sh, or shtool in gmp \"$srcdir\"/gmp" "$LINENO" 5
++  as_fn_error $? "cannot find install-sh, install.sh, or shtool in . \"$srcdir\"/." "$LINENO" 5
+ fi
+
+ # These three variables are undocumented and unsupported,
+diff -druN src.orig/src/configure.in src/src/configure.in
+--- src.orig/src/configure.in	2012-12-07 22:01:02.000000000 +0100
++++ src/src/configure.in	2014-04-09 15:17:50.282780900 +0200
+@@ -11,7 +11,7 @@
+ AC_INIT([ecl],[12.12.1],[])
+ AC_REVISION([$Revision$])
+ AC_CONFIG_SRCDIR([bare.lsp.in])
+-AC_CONFIG_AUX_DIR([gmp])
++AC_CONFIG_AUX_DIR([.])
+ AC_PREREQ(2.59)
+
+ dnl -----------------------------------------------------------------------

build/pkgs/ecl/spkg-install

@@ -70,6 +70,13 @@ export LDFLAGS
 # Building ECL in parallel doesn't work, so use only 1 thread
 MAKE="$MAKE -j1"
 
+# Currently config.[guess|sub] scripts are too old
+cp "$SAGE_ROOT"/config/config.* src/
+if [ $? -ne 0 ]; then
+    echo >&2 "Failed to copy up-to-date FSF config.* scripts from"
+    echo >&2 "\$SAGE_ROOT/config directory ... exiting"
+    exit 1
+fi
 
 if [ "`uname -sm`" = "SunOS i86pc" ] && [ "x$SAGE64" = xyes ]; then
     # Need to add --with-dffi=no to disable assembly code on OpenSolaris x64.

build/pkgs/ecl/spkg-src

@@ -35,9 +35,5 @@ rm -rf msvc contrib/encodings contrib/unicode
 cd src
 rm -rf gc-unstable libffi
 
-# Remove almost everything from gmp directory
-mv gmp gmp-remove
-# Save a few files
-mkdir gmp
-cp -p gmp-remove/config.* gmp-remove/configfsf.* gmp-remove/install*sh gmp
-rm -rf gmp-remove
+# Remove gmp directory
+rm -rf gmp

build/pkgs/git/package-version.txt

@@ -1 +1 @@
-1.8.4.4
+1.8.4.4.p0

build/pkgs/git/spkg-install

@@ -62,6 +62,7 @@ $MAKE GIT-VERSION-FILE
 # some systems, leading for example to a different "make" being used.
 echo "Configuring git..."
 ./configure --prefix="$SAGE_LOCAL" \
+            --libexecdir="$SAGE_LOCAL"/libexec \
             --with-python="$SAGE_LOCAL"/bin/python \
             --without-tcltk \
             --with-sane-tool-path=

build/pkgs/libgap/spkg-install

@@ -26,7 +26,7 @@ echo "GAP was configured with $GAParch_system"
 
 # location of the corresponding gap installation
 # only used for the testsuite
-CPPFLAGS="$CPPFLAGS"'-DSYS_DEFAULT_PATHS=\"'"$SAGE_LOCAL/gap/latest"'\"'
+CPPFLAGS="$CPPFLAGS"' -DSYS_DEFAULT_PATHS=\"'"$SAGE_LOCAL/gap/latest"'\"'
 
 cd src