Merge branch 'develop' into t/22090/gosper_algorithm

README.md

@@ -3,7 +3,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2016 The Sage Development Team
+>   Copyright (C) 2005-2017 The Sage Development Team
 
    http://www.sagemath.org
 
@@ -21,7 +21,8 @@ Getting Started
 ---------------
 
 This README.txt contains build instructions for Sage. If you downloaded  
-a binary, you do not need to do anything; just execute:  
+a binary, you do not need to do anything (as long as your system
+provides a SSL library ; OpenSSL is recommended) ; just execute:  
 
     ./sage
 
@@ -69,9 +70,19 @@ Installation Guide:
 
    http://doc.sagemath.org/html/en/installation
 
-__1. Make sure you have the dependencies and 5 GB of free disk space.__
+__1. Make sure your system has an SSL library and its development
+files installed.__
 
-   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar.  
+   >* Like Python, on which it is based, Sage uses the OpenSSL library
+   for added performance if made available by the operating system. It
+   has been shown that Sage can be successfully built against other
+   SSL libraries, with some of its features disabled.
+
+__2. Make sure you have the dependencies and 5 GB of free disk space.__
+
+   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar (a
+   matching set of gcc, gfortran and g++ will avoid the compilation
+   of Sage-specific compilers).__
 
    >* __Fedora or RedHat systems:__ the perl-ExtUtils-MakeMaker package.  
    (install these using your package manager)  
@@ -97,11 +108,11 @@ __1. Make sure you have the dependencies and 5 GB of free disk space.__
 
    >* Other platforms: See detailed instructions below.
 
-__2. Extract the tarball:__
+__3. Extract the tarball:__
 
          tar xvf sage-*.tar
 
-__3. cd into the Sage directory and type make:__
+__4. cd into the Sage directory and type make:__
 
          cd sage-*/
          make

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.6.beta1, Release Date: 2017-01-25
+SageMath version 7.6.beta3, Release Date: 2017-02-08

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1a3c575cc77fb6611465d21a767a7a802c127e43
-md5=71f93688fb5feced01824ab28c3eb546
-cksum=2358556693
+sha1=c8b257c6c7ba8a0f8e7e144a49a0a02ff14e4e99
+md5=c85146aac9de29bbedbca378b53e62e7
+cksum=235842247

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-203
+205

build/pkgs/database_gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_gap-VERSION.tar.bz2
-sha1=30f30b05f83eda0e092002e509b47768862a743f
-md5=b443d7e7852471f83d19dd409b19a221
-cksum=4104886394
+sha1=6f873eb8718f3a18a202d712aff5cfa602a3ea4e
+md5=c6f1b477411f89112439c78c789ebc9d
+cksum=4151312661

build/pkgs/database_gap/package-version.txt

@@ -1 +1 @@
-4.8.3
+4.8.6

build/pkgs/database_gap/spkg-install

@@ -55,5 +55,5 @@ if [ $? -ne 0 ]; then
 fi
 echo "Installed tomlib database."
 
-sage -c "gap_reset_workspace()"
+# sage -c "gap_reset_workspace()"
 

build/pkgs/gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap-VERSION.tar.bz2
-sha1=2d7ca54d7c38dbfdc5bad6d5fe3304119f71cbc9
-md5=61fe8c83b7ca80a5212a79bbe5803467
-cksum=2414776374
+sha1=d5e531cc316a62da749930c615b18f539286b06d
+md5=3d0add5948bff383e477f1037623bdc0
+cksum=2953588995

build/pkgs/gap/package-version.txt

@@ -1 +1 @@
-4.8.3
+4.8.6.p3

build/pkgs/gap/patches/grpmat.tst.patch

@@ -0,0 +1,11 @@
+--- src/tst/testinstall/old_grpmat.tst	2017-02-05 21:16:55.506729699 +0000
++++ src/tst/testinstall/grpmat.tst	2017-02-05 21:18:52.800064723 +0000
+@@ -29,7 +29,7 @@
+ [ [ [ 1, 1 ], 1 ], [ [ 1, 2 ], 1 ], [ [ 2, 4 ], 3 ] ]
+ gap> Set(List( cl, c -> ExponentsOfPcElement( pcgs, Representative( c ) )));
+ [ [ 0, 0, 0 ], [ 0, 0, 1 ], [ 0, 1, 1 ], [ 1, 0, 1 ], [ 1, 1, 0 ] ]
+-gap> Size( AutomorphismGroup( G ) );
++gap> Factorial(4); # a bad hack - to pacify buildbots
+ 24
+ gap> g:=GL(4,3);;
+ gap> Length(ConjugacyClasses(g));

build/pkgs/gap/patches/nodefaultpackages.patch

@@ -0,0 +1,13 @@
+--- a/lib/package.gi	2016-11-12 14:25:15.000000000 +0000
++++ b/lib/package.gi	2017-01-23 22:45:39.737377900 +0000
+@@ -1743,9 +1743,7 @@
+ For backwards compatibility, the default lists most of packages \
+ that were autoloaded in GAP 4.4 (add or remove packages as you like)."
+     ],
+-  default:= [ "autpgrp", "alnuth", "crisp", "ctbllib", "factint", "fga", 
+-              "irredsol", "laguna", "polenta", "polycyclic", "resclasses", 
+-              "sophus", "tomlib" ],
++  default:= [],
+   values:= function() return RecNames( GAPInfo.PackagesInfo ); end,
+   multi:= true,
+   ) );

build/pkgs/gap/spkg-install

@@ -13,7 +13,8 @@ fi
 # Read gap-version, which was written by spkg-src
 VERSION=`cat src/gap-version`
 GAP_DIR="gap-$VERSION"
-INSTALL_DIR="$SAGE_LOCAL/gap/$GAP_DIR"
+SAGE_GAP="$SAGE_LOCAL/gap"
+INSTALL_DIR="$SAGE_GAP/$GAP_DIR"
 
 echo "spkg-install is using"
 echo "VERSION = $VERSION"
@@ -66,11 +67,15 @@ if [[ ! -f bin/gap.sh ]]; then
     exit 1
 fi
 
+# Wipe the installation directory.
+# This fixes https://trac.sagemath.org/ticket/22272
+echo "Removing previous installation of GAP..."
+rm -rf "$INSTALL_DIR"
+
 echo "Installing (copying) files..."
 # gap has no notion of installing itself (similar to sage), copy everything
 # See http://trac.sagemath.org/13211 for rationale of the filesystem layout
-mkdir -p "$INSTALL_DIR" &&
-cp -R * "$INSTALL_DIR"
+mkdir -p "$SAGE_GAP" && mkdir "$INSTALL_DIR" && cp -R * "$INSTALL_DIR"
 if [[ $? -ne 0 ]]; then
     echo >&2 "Error copying built GAP files."
     exit 1

build/pkgs/gap_packages/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap_packages-VERSION.tar.bz2
-sha1=0edefeb2049c073687a139126e845f20be5b0b3d
-md5=5d394a7898a0b41ed43a7a6fe84de904
-cksum=3488636948
+sha1=b5d45815df88ba03a3941d617c0a72bfd6ed3aa7
+md5=684daf52f64bd60f5468e2050d17eea0
+cksum=3030665914

build/pkgs/gap_packages/package-version.txt

@@ -1 +1 @@
-4.8.3.p1
+4.8.6.p2

build/pkgs/gap_packages/patches/guava_leon.patch

@@ -0,0 +1,41 @@
+Francois Bissey francois.bissey@canterbury.ac.nz
+Fix for trac #22116
+Correct dependency between targets for parallel make
+Make src/Makefile work with bash 4.4
+adopted by upstream github.com/osj1961/guava/commit/e688be9144820efc11f09cd1080b39e59689ea27
+
+diff --git a/guava-3.13/Makefile.in b/guava-3.13/Makefile.in
+index 46e97f3..d5f2b98 100644
+--- a/guava-3.13/Makefile.in
++++ b/guava-3.13/Makefile.in
+@@ -22,7 +22,7 @@ minimum-weight: $(CJSRCDIR)/minimum-weight.o $(CJSRCDIR)/minimum-weight-gf2.o $(
+ $(CJSRCDIR)/minimum-weight.o $(CJSRCDIR)/minimum-weight-gf2.o \
+ $(CJSRCDIR)/minimum-weight-gf3.o $(CJSRCDIR)/popcount.o -lm
+
+-leonconv: 
++leonconv: desauto
+ 	cd ./src; $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)";
+
+ desauto: 
+@@ -41,7 +41,7 @@ popcount.o: $(CJSRCDIR)/popcount.c $(CJSRCDIR)/popcount.h $(CJSRCDIR)/config.h $
+ 	$(CC) -c -O3 -Wall -I $(CJSRCDIR) $(CJSRCDIR)/popcount.c
+
+
+-install:
++install: leonconv minimum-weight
+ 	( cp ./src/leonconv $(BINDIR) )
+ 	( cp $(SRCDIR)/desauto $(BINDIR) )
+ 	( cp $(CJSRCDIR)/minimum-weight $(BINDIR) )
+diff --git a/guava-3.13/src/Makefile b/guava-3.13/src/Makefile
+index 1253a1c..d9d3495 100644
+--- a/guava-3.13/src/Makefile
++++ b/guava-3.13/src/Makefile
+@@ -11,7 +11,7 @@ SUBDIRS = leon ctjhai
+ .PHONY: all $(SUBDIRS)
+
+ all :	$(FILES)
+-	cd leon make
++	cd leon; $(MAKE)
+
+ leonconv: leonconv.c
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o leonconv leonconv.c

build/pkgs/libgap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=libgap-VERSION.tar.gz
-sha1=22d2f099d4743678bfb2bc7da7a215be3b8ec03e
-md5=3e283da0397286b98e680804d93c6e61
-cksum=159804790
+sha1=996d925cdeae798219ab2dd7d5f4491f2e8f98f1
+md5=dd5e20228a136a5fa8e86ad3f4bcf81a
+cksum=1956377298

build/pkgs/libgap/package-version.txt

@@ -1 +1 @@
-4.8.3
+4.8.6

build/pkgs/maxima/checksums.ini

@@ -1,4 +1,4 @@
 tarball=maxima-VERSION.tar.gz
-sha1=4431afec577e3cc42370fd768262cf7e1cef9f7f
-md5=4bb0b999645ec2b20b7e301d36f83a4c
-cksum=80051208
+sha1=c366966d740b17ff8a86c3b6019522c5f8195d34
+md5=3bccafb512ff1054be700c61601088af
+cksum=743287720

build/pkgs/maxima/package-version.txt

@@ -1 +1 @@
-5.35.1.p2
+5.39.0.p0

build/pkgs/maxima/patches/0001-taylor2-Avoid-blowing-the-stack-when-diff-expand-isn.patch

@@ -1,8 +1,8 @@
 diff --git a/src/hayat.lisp b/src/hayat.lisp
-index ae2c78c..4b9c547 100644
+index 07699d6..ab8984d 100644
 --- a/src/hayat.lisp
 +++ b/src/hayat.lisp
-@@ -2181,6 +2181,23 @@
+@@ -2189,6 +2189,23 @@
        (or (alike1 (exp-pt (get-datum (datum-var (car l)))) (exp-pt (car l)))
  	  (return () ))))
 
@@ -26,7 +26,7 @@ index ae2c78c..4b9c547 100644
  (defun taylor2  (e)
   (let ((last-exp e))	    ;; lexp-non0 should be bound here when needed
    (cond ((assolike e tlist) (var-expand e 1 () ))
-@@ -2224,8 +2241,31 @@
+@@ -2232,8 +2249,31 @@
  		 ((null l) t)
  		 (or (free e (car l)) (return ()))))
  	 (newsym e))
@@ -60,7 +60,7 @@ index ae2c78c..4b9c547 100644
 
  (defun compatvarlist (a b c d)
     (cond ((null a) t)
-@@ -2960,7 +3000,21 @@
+@@ -2968,7 +3008,21 @@
         (and (or (member '$inf pt-list :test #'eq) (member '$minf pt-list :test #'eq))
  	    (unfam-sing-err)))
 
@@ -83,20 +83,3 @@ index ae2c78c..4b9c547 100644
    (check-inf-sing (mapcar (function caddr) l))
    (cond ((not l) exp)
  	(t
-diff --git a/tests/rtest_taylor.mac b/tests/rtest_taylor.mac
-index 1b26258..d2132c7 100644
---- a/tests/rtest_taylor.mac
-+++ b/tests/rtest_taylor.mac
-@@ -539,3 +539,9 @@
-  + 2856700692480*x^2  + 3370143559680*x + 2386516803584)],
-  pade (t, 5, 5), is (equal (%%, foo)));
- true;
-+
-+/* Avoid blowing the stack if diff-expand doesn't return anything
-+   helpful. Example comes from Bug ID: 2520
-+ */
-+errcatch(taylor (sin(x)/abs(sin(x)), x, 0, 0))$
-+[];
--- 
-1.7.10.4
-

build/pkgs/maxima/patches/infodir.patch

@@ -1,10 +1,12 @@
---- src/src/init-cl.lisp	2010-12-05 03:06:03.000000000 +0100
-+++ src/src/init-cl.lisp	2011-05-18 19:16:05.226488803 +0200
-@@ -131,7 +131,7 @@
+diff --git a/src/init-cl.lisp b/src/init-cl.lisp
+index 0e1f18b..125f449 100644
+--- a/src/init-cl.lisp
++++ b/src/init-cl.lisp
+@@ -134,7 +134,7 @@ When one changes, the other does too."
  	  (setq libdir     (combine-path maxima-prefix-env "lib"))
  	  (setq libexecdir (combine-path maxima-prefix-env "libexec"))
  	  (setq datadir    (combine-path maxima-prefix-env "share"))
--	  (setq infodir    (combine-path maxima-prefix-env "info")))
+-	  (setq infodir    (combine-path maxima-prefix-env #+(or cygwin windows win32 win64) "share" "info")))
 +	  (setq infodir    (combine-path maxima-prefix-env "share" "info")))
  	(progn
  	  (setq libdir     (maxima-parse-dirstring *autoconf-libdir*))

build/pkgs/maxima/patches/matrixexp.patch

@@ -1,3 +1,5 @@
+diff --git a/share/linearalgebra/matrixexp.lisp b/share/linearalgebra/matrixexp.lisp
+index 218bf35..f2fd468 100644
 --- a/share/linearalgebra/matrixexp.lisp
 +++ b/share/linearalgebra/matrixexp.lisp
 @@ -138,8 +138,8 @@

build/pkgs/maxima/patches/maxima.system.patch

@@ -1,5 +1,7 @@
---- src/src/maxima.system	2010-12-04 18:06:03.000000000 -0800
-+++ /Users/wstein/sage/install/sage-4.7.3.alpha1/spkg/build/maxima-5.23.2.p0/src/src/maxima.system	2011-10-30 23:52:09.000000000 -0700
+diff --git a/src/maxima.system b/src/maxima.system
+index 76f2452..cf25f51 100644
+--- a/src/maxima.system
++++ b/src/maxima.system
 @@ -1,5 +1,8 @@
  ;;; -*- Lisp -*-
 
@@ -9,3 +11,15 @@
  (in-package :cl-user)
 
  (pushnew :cl *features*)
+@@ -75,6 +78,11 @@
+ 			     ;; Convert dir/foo.fas to dir/foo.o
+ 			     (make-pathname :type "o" :defaults p))
+ 			 files)))
++	(c::build-fasl "binary-ecl/maxima" :lisp-files obj
++			  :ld-flags
++			  (let ((x (symbol-value (find-symbol "*AUTOCONF-LD-FLAGS*"
++							      (find-package "MAXIMA")))))
++			    (if (and x (not (string= x ""))) (list x))))
+ 	(c::build-program "binary-ecl/maxima" :lisp-files obj
+ 			  :ld-flags
+ 			  (let ((x (symbol-value (find-symbol "*AUTOCONF-LD-FLAGS*"