Merge branch 'develop' into u/tscrim/rc_bij_pdf

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta2, released 2014-05-24
+Sage version 6.3.beta3, released 2014-06-04

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=56399592db642ce25cd331edba8ceeecfa211393
-md5=030561c77e141c8e0c7c045b1c301964
-cksum=4180963490
+sha1=94c4a9dc954e0d5653907a5187f61059835c713b
+md5=9316e8ffe91a749ea737da0f57f3f1ef
+cksum=66239435

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-31
+33

build/pkgs/database_cremona_ellcurve/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_cremona_ellcurve-VERSION.tar.bz2
-sha1=25f256d78bf5c4454d85bb9a22df2d396e4962ba
-md5=14de1b11227fdd66e1a87e8101940988
-cksum=2753267872
+sha1=ab96f509574419c03d9f1c8820c4d96042a17a04
+md5=56956829063534142f9f12bc1274c01c
+cksum=2400753722

build/pkgs/database_cremona_ellcurve/package-version.txt

@@ -1 +1 @@
-20140325
+20140512

build/pkgs/gap_packages/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap_packages-VERSION.tar.bz2
-sha1=8fbd475be3aec265e36a600fe9cf3b00bd131d88
-md5=8d3c0fa85af6528bf2b9faf491da4180
-cksum=1526641510
+sha1=9ce61e1947bc5aa0f761f97fb9777e97ab6d3eda
+md5=57657e75f9b80f5afc36dcdd3538eada
+cksum=2009528425

build/pkgs/gap_packages/package-version.txt

@@ -1 +1 @@
-4.7.4
+4.7.4.20140531

build/pkgs/gap_packages/spkg-install

@@ -31,7 +31,7 @@ cd src/
 for p in \
     crime ctbllib design factint grape \
     guava-3.12 Hap1.10 HAPcryst laguna polymaking \
-    sonata toric1.8 polycyclic-2.11 autpgrp Alnuth-3.0.0
+    sonata toric1.8 polycyclic-2.11 autpgrp Alnuth-3.0.0 atlasrep
 do
     echo "Copying package $p"
     $CP -pr $p "$PKG_DIR"

build/pkgs/maxima/SPKG.txt

@@ -29,43 +29,55 @@ COPYING.
 
  * The Maxima mailing list - see http://maxima.sourceforge.net/maximalist.html
 
+== Dependencies ==
+
+ * ECL (Embedded Common Lisp)
+
 == Special Update/Build Instructions ==
 
- * Make sure the patches still apply cleanly.
+1. Go to http://sourceforge.net/projects/maxima/files/Maxima-source/
+   and download the source tarball maxima-x.y.z.tar.gz.
+
+2. Extract the tarball.
+
+3. In the directory maxima-x.y.z, run the spkg-src script.
+
+4. Compress the directory into a new file maxima-x.y.z.tar.bz2 and
+   place it in the upstream/ directory.
 
- * Run the `spkg-src` script after updating to a newer upstream
-   release. It removes a large amount of unused documentation and
-   disables the associated Makefiles, reducing the size of the SPKG
-   greatly.
+5. Make sure the patches still apply cleanly, and update them if
+   necessary.
 
-=============================================================
+6. Test the resulting package.
 
-How to make a new version of the Maxima spkg.
+Here's what spkg-src does:
 
-  1. Go to http://sourceforge.net/project/showfiles.php?group_id=4933
-     and download the source tar.gz ball.  That's near the bottom
-     of that page (i.e., hard to find if you don't scroll past
-     all the big red adds).
+ * Removes the unneeded PDF figures from the documentation.
 
-  2. Extract the tarball to replace the src/ subdirectory of this package.
+ * Removes the foreign language versions of the info files.
 
-  3. Create an spkg from this directory, with
-        sage -pkg maxima-x.y.z
+The following patches are applied:
 
-  4. Test the resulting maxima-??.spkg.
+ * 0001-taylor2-Avoid-blowing-the-stack-when-diff-expand-isn.patch:
+   Fix for Maxima bug #2520 (abs_integrate fails on abs(sin(x)) and
+   abs(cos(x))).  Introduced in Trac #13364 (Upgrade Maxima to
+   5.29.1).
 
-=============================================================
+ * build-fasl.patch: Build a fasl library for ecl in addition to an
+   executable program.  Introduced in Trac #16178 (Build maxima fasl
+   without asdf).
 
-Here's what spkg-dist does:
+ * infodir.patch: Correct the path to the Info directory.
 
-* Removes the foreign language versions of the info files,
-  since they add several MEGS (and they weren't in previous
-  versions of Maxima).  This means making empty directories
-  and changing the Makefile.in's.
+ * matrixexp.patch: Fix matrixexp(matrix([%i*%pi])), which broke after
+   Maxima 5.29.1.  Introduced in Trac #13973.
 
-* In the past, before doing step 3 above, one would also type
+ * maxima_bug_2526.patch: Fix for Maxima bug #2526 (abs_integrate
+   fails on integrate(sqrt(x + sqrt(x)), x)).  Introduced in Trac
+   #13364 (Upgrade Maxima to 5.29.1).
 
-       ./spkg-dist
+ * maxima.system.patch: Set c::*compile-in-constants* to t.
 
-  However, this caused problems with calling automake because
-  of the changed .in files.
+ * undoing_true_false_printing_patch.patch: Revert an upstream change
+   causing '?' to be printed around some words.  Introduced in Trac
+   #13364 (Upgrade Maxima to 5.29.1).

build/pkgs/maxima/checksums.ini

@@ -1,4 +1,4 @@
 tarball=maxima-VERSION.tar.bz2
-sha1=9314e23a4166a3d455b37a18d846474aa310e6c4
-md5=40b01a718ddba1c8364d76a1e5d35d8f
-cksum=2999621606
+sha1=8c1a10d0cfb10bb10448fd18b021d73e25fc744a
+md5=55140d4f9f7f212fb1cf8479b895862e
+cksum=1303222960

build/pkgs/maxima/package-version.txt

@@ -1 +1 @@
-5.29.1.p5
+5.33.0.p0

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

@@ -87,10 +87,10 @@ 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
-@@ -517,3 +517,9 @@ diff('(f(taylor(x,x,0,6))),x);
- 'diff(f(taylor(x,x,0,6)),x,1);
- ev(%,nouns);
- 'diff(f(+x),x,1);
+@@ -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

build/pkgs/maxima/patches/matrixexp.patch

@@ -0,0 +1,13 @@
+--- a/share/linearalgebra/matrixexp.lisp	2013-10-07 04:37:12.000000000 +0100
++++ b/share/linearalgebra/matrixexp.lisp	2014-05-16 02:16:09.112011893 +0100
+@@ -138,8 +138,8 @@
+ 	   (print `(ratvars = ,$ratvars gcd = '$gcd algebraic = ,$algebraic))
+ 	   (print `(ratfac = ,$ratfac))
+ 	   (merror "Unable to find the spectrum")))
+-   
+-    (setq res ($fullratsimp (ncpower (sub (mult z ($ident n)) mat) -1) z))
++
++    (setq res ($fullratsimp ($invert (sub (mult z ($ident n)) mat) '$crering) z))
+     (setq m (length sp))
+     (dotimes (i m)
+       (setq zi (nth i sp))

build/pkgs/maxima/patches/maxima_bug_2526.patch

@@ -11,7 +11,7 @@
      q : almost_everywhere_simp(q), 
 --- a/share/contrib/integration/rtest_abs_integrate.mac
 +++ b/share/contrib/integration/rtest_abs_integrate.mac
-@@ -511,16 +511,24 @@ integrate(sqrt(max(5,x)),x);
+@@ -510,12 +510,19 @@ integrate(sqrt(max(5,x)),x);
  /* abs_integrate causes stack overflow - ID: 3533723 */
  block([extra_integration_methods : ['intfudu, 'intfugudu, 'signum_int, 'abs_integrate_use_if, 'floor_int, 'if_int]],
     integrate(log(sin(x)),x));
@@ -35,10 +35,5 @@
 +integrate(sqrt(x + sqrt(x)),x,0,1);
 +(3*log(sqrt(2)+1)-3*log(sqrt(2)-1)+7*2^(3/2))/24$
 
- (print("time = ", elapsed_real_time () - start), is(elapsed_real_time () - start < 70));
- true$
+ /* SF bug #2557: "abs_integrate leaks assumptions into enclosing context" */
 
-+
- (remvalue(e,i,di,f1,start), remove(x,noninteger), remfunction(convolution, unit_box),0);
- 0$ 
-

build/pkgs/maxima/spkg-src

@@ -8,8 +8,8 @@ def cmd(x):
     if os.system(x):
         print "(Failed.)"
 
-cmd('rm src/doc/info/figures/*.pdf')
+cmd('rm doc/info/figures/*.pdf')
 
 for X in ['de', 'de.utf8', 'es', 'es.utf8', 'pt', 'pt.utf8', 'pt_BR', 'pt_BR.utf8']:
-    cmd('rm -r src/doc/info/%s/*'%X)
-    open('src/doc/info/%s/Makefile.in'%X,'w').write('all:\n\tls\n\n')
+    cmd('rm -r doc/info/%s/*'%X)
+    open('doc/info/%s/Makefile.in'%X,'w').write('all:\n\tls\n\n')

build/pkgs/mcqd/SPKG.txt

@@ -0,0 +1,29 @@
+= MCQD 1.0 =
+
+== Description ==
+
+MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an
+undirected graph.
+
+== License ==
+
+GPL 3
+
+== SPKG Maintainers ==
+
+Jernej Azarija ([email protected])
+Nathann Cohen  ([email protected])
+
+== Upstream Contact ==
+
+MCQD is currently being maintained by Janez Konc.
+http://www.sicmm.org/~konc/
+
+== Dependencies ==
+
+None
+
+== Changelog ==
+
+=== mcqd-1.0 (Jernej Azarija, Nathann Cohen, 19 march 2014) ==
+ * Initial version

build/pkgs/mcqd/checksums.ini

@@ -0,0 +1,4 @@
+tarball=mcqd-VERSION.tar.bz2
+sha1=9c55da46815aa3903f0be2d1ffbdff9c17d4aa31
+md5=831538634b7b7efe15b5e5ad3d9c59c2
+cksum=2853560422

build/pkgs/mcqd/package-version.txt

@@ -0,0 +1 @@
+1.0

build/pkgs/mcqd/spkg-install

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+cd src
+grep -v "std..cout.*current max" mcqd.h > mcqd2.h &&
+mv mcqd2.h mcqd.h &&
+g++ -O3 -c mcqd.cpp -o $SAGE_LOCAL/lib/libmcqd.so &&
+cp mcqd.h $SAGE_LOCAL/include/mcqd.h
+
+if [ $? -ne 0 ]; then
+    echo "An error occurred whilst building MCQD"
+    exit 1
+fi

build/pkgs/pexpect/SPKG.txt

@@ -37,6 +37,9 @@ Patches:
 
 == Changelog ==
 
+=== pexpect-2.0.p6 (Bradly Schlenker, 10 May 2014) ===
+ * Trac #15178: Fixed pexpect.py-isdir_bug_fix.patch. (mislabeled variable)
+
 === pexpect-2.0.p5 (Jeroen Demeyer, 13 January 2012) ===
  * Trac #12221: add env.patch to add env parameter to spawn.__init__()
  * Restore upstream sources, use patch for patching

build/pkgs/pexpect/package-version.txt

@@ -1 +1 @@
-2.0.p5
+2.0.p6

build/pkgs/pexpect/patches/pexpect.py-isdir_bug_fix.patch

@@ -5,7 +5,7 @@
      # Special case where filename already contains a path.
      if os.path.dirname(filename) != '':
 -        if os.access (filename, os.X_OK):
-+        if os.access (filename, os.X_OK) and not os.path.isdir(f):
++        if os.access (filename, os.X_OK) and not os.path.isdir(filename):
              return filename
 
      if not os.environ.has_key('PATH') or os.environ['PATH'] == '':