Trac #15767: Upgrade PARI to 2.7.1

'''Upstream''':
[http://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.7.1.tar.gz]

'''Updated''' (changes have always been made directly in the source
tarball and the package will be removed anyway in #15808): [http://boxen
.math.washington.edu/home/jdemeyer/spkg/genus2reduction-20140211.tar.bz2
]

URL: http://trac.sagemath.org/15767
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Peter Bruin

Author: Release Manager

build/pkgs/genus2reduction/checksums.ini

@@ -1,4 +1,4 @@
 tarball=genus2reduction-VERSION.tar.bz2
-sha1=a29ae793b4c2d427ed5ffbecce4f77f5ba5c1e36
-md5=550356571d56cb887cc6a7c035e941e5
-cksum=649238856
+sha1=df358e78da17ce74cd5b63f379e7f7f91c21f08e
+md5=46bd298ef0699d7fb7763d08228a3ce1
+cksum=2690437212

build/pkgs/genus2reduction/package-version.txt

@@ -1 +1 @@
-0.3.p8
+20140211

build/pkgs/lcalc/SPKG.txt

@@ -82,8 +82,8 @@ http://code.google.com/p/l-calc/
      to not redefine the double() cast, thats just fragile and will sooner or
      later again fail inside some system headers.
 
- * pari-2.4.4.patch:
-   Replace obsolete lgeti() by (long)cgeti().
+ * pari-2.7.patch:
+   Various changes to port to PARI 2.7.
 
  * init_stack.patch:
    Replace obsolete allocatemoremem() by a direct call to the private

build/pkgs/lcalc/package-version.txt

@@ -1 +1 @@
-1.23.p12
+1.23.p13

build/pkgs/lcalc/patches/pari-2.4.4.patch build/pkgs/lcalc/patches/pari-2.7.patch

@@ -17,3 +17,15 @@
 
      //gaffsg(a1,(GEN) F[1]);
      //gaffsg(a2,(GEN) F[2]);
+diff -ru src/src/Lcommandline_elliptic.cc b/src/Lcommandline_elliptic.cc
+--- src/src/Lcommandline_elliptic.cc	2014-02-10 10:17:11.004419528 +0100
++++ b/src/Lcommandline_elliptic.cc	2014-02-10 10:20:37.757715491 +0100
+@@ -139,7 +139,7 @@
+     gaffect(strtoGEN(a4), (GEN) F[4]);
+     gaffect(strtoGEN(a6), (GEN) F[5]);
+ 
+-    E = initell(F,BIGDEFAULTPREC);
++    E = ellinit(F, NULL, BIGDEFAULTPREC);
+ 
+     C=globalreduction(E);
+ 

build/pkgs/pari/SPKG.txt

@@ -28,7 +28,8 @@ GPL version 2+
  * http://pari.math.u-bordeaux.fr/
 
 == Dependencies ==
- * MPIR (in place of GMP)
+ * Perl
+ * MPIR or GMP
  * Readline
  * GNU patch (shipped with Sage)
 

build/pkgs/pari/checksums.ini

@@ -1,4 +1,4 @@
-tarball=pari-VERSION.tar.bz2
-sha1=3f0838940fcf1cb7748979fe16e4b5cab0d19080
-md5=4c54710f7e2d4de7b8781edb9d604c60
-cksum=2949888924
+tarball=pari-VERSION.tar.gz
+sha1=7edec0dfefc5d0c47a7f1c2fb1016cfe313c1652
+md5=cdf11f569140343449bda477bea19ddb
+cksum=1676608517

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.5.5b.p1
+2.7.1.p0

build/pkgs/pari/patches/GCC_PR49330.patch

@@ -1,22 +1,22 @@
-diff -ru src/src/language/init.c src.patched/src/language/init.c
---- a/src/language/init.c     2012-02-11 10:57:38.000000000 +0100
-+++ b/src/language/init.c     2012-03-07 10:24:37.000000000 +0100
-@@ -593,14 +593,16 @@
+diff -ru src/src/language/init.c b/src/language/init.c
+--- src/src/language/init.c	2014-02-01 16:29:48.955825926 +0100
++++ b/src/language/init.c	2014-02-01 16:31:24.612818588 +0100
+@@ -612,14 +612,16 @@
  pari_init_functions(void)
  {
-   stack_init(&s_MODULES, sizeof(*MODULES),(void**)&MODULES);
--  stack_pushp(&s_MODULES,functions_basic);
-   stack_init(&s_OLDMODULES, sizeof(*OLDMODULES),(void**)&OLDMODULES);
--  stack_pushp(&s_OLDMODULES,oldfonctions);
+   pari_stack_init(&s_MODULES, sizeof(*MODULES),(void**)&MODULES);
+-  pari_stack_pushp(&s_MODULES,functions_basic);
+   pari_stack_init(&s_OLDMODULES, sizeof(*OLDMODULES),(void**)&OLDMODULES);
+-  pari_stack_pushp(&s_OLDMODULES,oldfonctions);
    functions_hash = (entree**) pari_calloc(sizeof(entree*)*functions_tblsz);
    pari_fill_hashtable(functions_hash,
                        new_fun_set? functions_basic: oldfonctions);
    defaults_hash = (entree**) pari_calloc(sizeof(entree*)*functions_tblsz);
    pari_add_defaults_module(functions_default);
 +  /* Move this down to work around GCC bug
 +   * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49330 */
-+  stack_pushp(&s_MODULES,functions_basic);
-+  stack_pushp(&s_OLDMODULES,oldfonctions);
++  pari_stack_pushp(&s_MODULES,functions_basic);
++  pari_stack_pushp(&s_OLDMODULES,oldfonctions);
  }
-
+ 
  void

build/pkgs/pari/patches/KERNELCFLAGS.patch

@@ -1,10 +1,10 @@
 diff -ru src/config/get_cc b/config/get_cc
---- src/config/get_cc	2012-09-25 23:10:46.000000000 +0200
-+++ b/config/get_cc	2013-01-07 16:02:46.607514084 +0100
-@@ -122,7 +122,11 @@
-   case "$__gnuc__" in
-     2.95.[3-9]*|[3-9].*) OPTFLAGS="$OPTFLAGS -fno-strict-aliasing";;
-   esac
+--- src/config/get_cc	2014-02-01 21:41:54.534348273 +0100
++++ b/config/get_cc	2014-02-01 21:42:50.850930971 +0100
+@@ -94,7 +94,11 @@
+     OPTFLAGS="$OPTFLAGS -fno-strict-aliasing"
+   fi
+   rm -f $exe $exe$exe_suff
 -  KERNELCFLAGS=-funroll-loops
 +  if [ "$SAGE_DEBUG" = yes ]; then
 +    KERNELCFLAGS=-O1

build/pkgs/pari/patches/README.txt

@@ -4,32 +4,17 @@ Current patches to PARI in Sage:
 
 Patches to configuration files:
 * get_ld.patch (Carl Witty): Disable -rpath.
-* get_tests.patch (John Cremona): Disable testing of ellglobalred in
-  "make test-all" in spkg-check, since it requires the elldata database
-  which we do not include since it is about 18MB.
 * get_config_options.patch (Leif Leonhardy): Catch invalid arguments to
   "--graphic" (and treat such as an error) since otherwise strange
   compilation errors might occur (cf. #9722, too).
-* get_fltk.patch (Leif Leonhardy): Explicitly link against libstdc++
-  when using FLTK (for plotting) to support Fedora 13, and do an extra
-  check for the FLTK include dir (cf. #9722).
-* get_X11.patch (Leif Leonhardy): Also search */lib64/* for X11
-  libraries (since on some systems this is really a separate directory,
-  i.e. neither a symbolic link to */lib/* nor the target of a symbolic
-  link */lib/*; cf. #9722, too).
+* get_fltk.patch (Leif Leonhardy): do an extra check for the FLTK
+  include dir (cf. #9722).
 * get_dlcflags.patch (Jeroen Demeyer): Add -fno-common to DLCFLAGS on
   Darwin. Submitted upstream, but upstream only applied it for PowerPC.
   Since this doesn't break anything and only improves performance, add
   the flag unconditionally.
-* install_doc_no_make.patch (Jeroen Demeyer): Do not *build* the
-  documentation when doing install-doc or install-docpdf.  We must not
-  build the documentation because that requires tex.  On the other hand,
-  to have ? and ?? work within gp, we must install the .tex files (but
-  not .dvi files).  So simply not doing install-doc doesn't work.
 * perl_path.patch (Jeroen Demeyer): change first line of all perl
   scripts to "#!/usr/bin/env perl" (#10559).
-* cygwin_dll_a.patch (Jean-Pierre Flori): copy libpari.dll.a on Cygwin
-  (see #13333).
 * KERNELCFLAGS.patch (Jeroen Demeyer): when SAGE_DEBUG=yes, compile
   kernel files with -O1 instead of -funroll-loops; -O0 gives a
   segmentation fault on some OS X systems when doing
@@ -45,22 +30,6 @@ C files:
   gcc-4.6.3. Discussed with upstream:
   - http://pari.math.u-bordeaux.fr/archives/pari-dev-1203/msg00001.html
   - http://pari.math.u-bordeaux.fr/archives/pari-dev-1202/msg00006.html
-* trac_13902_determinant.patch (Jeroen Demeyer): patch backported from
-  upstream git repository based on commits
-  - 28ea998bc661f5bbde18b6d6b0f50111a10ae16c
-  - 249432f7088bfa114ed5cd3a5d64ef51ee968e35
-* polred.patch (Jeroen Demeyer): Fix polred(), add polredbest()
-  backported from upstream commits
-  - 2d00a24fbb1ffe8eba35b9a04763e36eef8a5f7b
-  - a3596c56f9439144a0dbed4c47bd6ff9485e3fc8
-  - 1a00ca416de4daebccaab2be1a4b8a061a9f2fde
-  - ad550d9bbfee8113087407c3262bffc27a020c98
-* q_eint1.patch (Jeroen Demeyer): Fix precision of eint1(), backported
-  from upstream commits
-  - b894e0171112493bb4945a6a0e4af039b54a1d1f
-  - 54eb37055167dbd8d4856b1bd698cf7018db561b
-  and completely backport new algorithm for mpveceint1(). The prefix
-  q_ in the patch filename is to ensure it comes after polred.patch.
 * det_garbage.patch (Jeroen Demeyer, #15654): When computing a
   determinant(), only collect garbage once per outer loop iteration.
   Better increase PARI stack size instead of collecting garbage too

build/pkgs/pari/patches/cygwin_dll_a.patch

@@ -1,51 +1,49 @@
-Binary files src/Olinux-x86_64/alglin1.o and b/Olinux-x86_64/alglin1.o differ
-Only in src/Olinux-x86_64: libpari-gmp.so.2.5.5
 diff -ru src/src/basemath/alglin1.c b/src/basemath/alglin1.c
---- src/src/basemath/alglin1.c	2014-01-09 15:43:35.847263581 +0100
-+++ b/src/basemath/alglin1.c	2014-01-09 15:55:47.903649326 +0100
-@@ -2412,6 +2412,7 @@
+--- src/src/basemath/alglin1.c	2014-01-29 18:00:27.000000000 +0100
++++ b/src/basemath/alglin1.c	2014-02-09 01:54:37.676725196 +0100
+@@ -247,6 +247,7 @@
    a = RgM_shallowcopy(a);
    for (i=1; i<nbco; i++)
    {
 +    int garbage = 0;  /* Only gerepile() once per loop iteration */
      for(k=i; k<=nbco; k++)
      {
-       gcoeff(a,k,i) = modii(gcoeff(a,k,i), p);
-@@ -2435,7 +2436,7 @@
+       gcoeff(a,k,i) = ff->red(E,gcoeff(a,k,i));
+@@ -271,7 +272,7 @@
        for (j=i+1; j<=nbco; j++)
        {
-         gcoeff(a,j,k) = Fp_sub(gcoeff(a,j,k), Fp_mul(m,gcoeff(a,j,i),p),p);
+         gcoeff(a,j,k) = ff->add(E, gcoeff(a,j,k), ff->mul(E,m,gcoeff(a,j,i)));
 -        if (low_stack(lim, stack_lim(av,1)))
 +        if (low_stack(lim, stack_lim(av,1)) && (garbage++ == 0))
          {
            if(DEBUGMEM>1) pari_warn(warnmem,"det. col = %ld",i);
-           gerepileall(av,2, &a,&x);
-@@ -2994,6 +2995,7 @@
+           gerepileall(av,4, &a,&x,&q,&m);
+@@ -3721,6 +3722,7 @@
    a = RgM_shallowcopy(a);
    for (i=1; i<nbco; i++)
    {
 +    int garbage = 0;  /* Only gerepile() once per loop iteration */
      k = pivot(a, data, i, NULL);
      if (k > nbco) return gerepilecopy(av, gcoeff(a,i,i));
      if (k != i)
-@@ -3013,7 +3015,7 @@
+@@ -3740,7 +3742,7 @@
        for (j=i+1; j<=nbco; j++)
        {
          gcoeff(a,j,k) = gsub(gcoeff(a,j,k), gmul(m,gcoeff(a,j,i)));
--        if (low_stack(lim, stack_lim(av,1)))
-+        if (low_stack(lim, stack_lim(av,1)) && (garbage++ == 0))
+-        if (low_stack(lim, stack_lim(av,3)))
++        if (low_stack(lim, stack_lim(av,3)) && (garbage++ == 0))
          {
            if(DEBUGMEM>1) pari_warn(warnmem,"det. col = %ld",i);
            gerepileall(av,2, &a,&x);
-@@ -3063,6 +3065,7 @@
+@@ -3791,6 +3793,7 @@
    {
      GEN ci, ck, m;
      int diveuc = (gequal1(pprec)==0);
 +    int garbage = 0;  /* Only gerepile() once per loop iteration */
 
      p = gcoeff(a,i,i);
      if (gequal0(p))
-@@ -3099,7 +3102,7 @@
+@@ -3827,7 +3830,7 @@
            GEN p1 = gsub(gmul(p,gel(ck,j)), gmul(m,gel(ci,j)));
            if (diveuc) p1 = mydiv(p1,pprec);
            gel(ck,j) = gerepileupto(av2, p1);

build/pkgs/pari/patches/det_garbage.patch

@@ -8,27 +8,27 @@
 +  -graphic|--graphic)
 +      shift; which_graphic_lib="$1"
 +      case "$which_graphic_lib" in
-+        auto|none|X11|qt|Qt|fltk|win32) ;;
++        auto|none|X11|qt|Qt|fltk|ps|win32) ;;
 +        *) echo "*** Unrecognized graphic lib \"$which_graphic_lib.\"" >&2
 +           error=true;;
 +      esac;;
    --graphic=*|--graphi=*|--graph=*|--grap=*|--gra=*|--gr=*|--g=*)
 -	       which_graphic_lib=`echo "$1" | sed -e 's/[-a-z]*=//'`;;
 +      which_graphic_lib=`echo "$1" | sed -e 's/[-a-z]*=//'`
 +      case "$which_graphic_lib" in
-+        auto|none|X11|qt|Qt|fltk|win32) ;;
++        auto|none|X11|qt|Qt|fltk|ps|win32) ;;
 +        *) echo "*** Unrecognized graphic lib \"$which_graphic_lib.\"" >&2
 +           error=true;;
 +      esac;;
 
    --without-readline|--with-readline=no) without_readline=yes ;;
    --with-readline) with_readline=yes ;;
-@@ -126,7 +137,7 @@
+@@ -139,7 +139,7 @@
  Build Options:
    --host=<arch-osname>  target achitecture
    --kernel=<kern>       kernel used
--  --graphic=<gr>        graphic library used (none X11 Qt fltk win32)
-+  --graphic=<gr>        graphic library used (none X11 qt Qt fltk win32 auto)
-   --time=<fun>          timing function to use (getrusage times ftime)
+-  --graphic=<gr>        graphic library used (none, X11, Qt, fltk, ps, win32)
++  --graphic=<gr>        graphic library used (none, X11, Qt, fltk, ps, win32, auto)
+   --time=<fun>          timing function to use (getrusage, clock_gettime,
+                           times, ftime)
    --builddir=<dir>      directory where the object files will be created
-   --tune                tune the binary for compiling host (slow)

build/pkgs/pari/patches/get_X11.patch

@@ -1,30 +1,19 @@
---- a/config/get_fltk	2010-11-04 14:51:50.910510930 +0100
-+++ b/config/get_fltk	2010-11-04 14:59:12.158786073 +0100
-@@ -10,18 +10,24 @@
-    fi
-    ;;
- *) if test ! -d "$with_fltk"; then
--    echo "### FLTK directory '$with_fltk' not found"
-+    echo "### Specified FLTK directory '$with_fltk' not found"
-   else
-     FLTKDIR=$with_fltk
+diff -ru src/config/get_fltk b/config/get_fltk
+--- src/config/get_fltk	2014-02-01 16:36:02.492702307 +0100
++++ b/config/get_fltk	2014-02-01 16:43:22.183289684 +0100
+@@ -16,8 +16,15 @@
    fi;;
  esac
  if test -n "$FLTKDIR"; then
--  echo "Using FLTK library, FLTKDIR = $FLTKDIR"
 +  if test -d "$FLTKDIR/include/FL"; then
-+    echo "Using FLTK library, FLTKDIR = \"$FLTKDIR\""
+   echo "Using FLTK library, FLTKDIR = $FLTKDIR"
+   FLTK_LIBS="`fltk-config --ldflags` -lstdc++"
 +  else
 +    echo "### Found the FLTK library, but not the necessary headers."
 +    echo "### Building without FLTK support."
 +    FLTKDIR=""
++    FLTK_LIBS=""
 +  fi
  else
    echo "### FLTK not found. Building without FLTK support"
- fi
- case "$osname" in
-   cygwin) FLTK_LIBS="-lgdi32 -lole32 -luuid -lwsock32 -lsupc++" ;;
-   darwin) FLTK_LIBS="-framework Carbon -lsupc++" ;;
--  *)      FLTK_LIBS="$X11_LIBS" ;;
-+  *)      FLTK_LIBS="$X11_LIBS -lstdc++" ;;
- esac
+   FLTK_LIBS=