Merge branch 'master' into ticket/15278

* master: (162 commits) [FIXUP] 5.13.beta4: update git specific files 5.13.beta4 5.13.beta4 [FIXUP] 5.13.beta3: update git specific files 5.13.beta3 5.13.beta3 Trac #15402: fix eint1() precision #14706: fix visibility of symbols for built-in libintl. also remove untracked directories after an aborted import patch trac_interface: encode fields with utf-8 as well sage.dev: don't textwrap during doctesting patch.py: deal with hg's silly copy commands remove reference to sage/misc/hg from docbuild SageDev: fix pull doctest SageDev: remove branch keyword from pull fix doctest errors in SageDev.push remove (now) bad uses of SageDev.pull remove unused garbage dumb down pull to fix it don't abort ticket editing on nop push ...
sagemath · Dec 6, 2013 · 126b036 · 126b036
2 parents c774057 + 0c6fcdf
commit 126b036
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diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,52 @@
 /local
 /logs
 /upstream
+
+###################
+# Temporary Files #
+###################
+
+# Various editors
+*~
+
+# Emacs
+\#*\#
+.\#*
+
+# Vim
+*.s[a-w][a-z]
+*.un~
+.netrwhist
+
+# PyCharm
+.idea
+.iml
+
+# Eclipse
+*.pydevproject
+.project
+.metadata
+*.tmp
+*.bak
+*.swp
+*~.nib
+.classpath
+.settings/
+.loadpath
+.externalToolBuilders/
+.cproject
+.buildpath
+
+# OSX specific temporary files
+.DS_Store
+._*
+.AppleDouble
+.LSOverride
+.Spotlight-V100
+.Trashes
+
+# Windows
+$RECYCLE.BIN/
+
+# SublimeText
+*.sublime-workspace
diff --git a/Makefile b/Makefile
@@ -21,6 +21,12 @@ build: logs
 		"tee -a ../logs/install.log"
 	./sage -b
 
+# Preemptively download all standard upstream source tarballs.
+download:
+	export SAGE_ROOT=$$(pwd) && \
+	export PATH=$$SAGE_ROOT/src/bin:$$PATH && \
+	./src/bin/sage-download-upstream
+
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
 # running the secure notebook. This make target requires internet
 # access. Note that this requires that your system have OpenSSL

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-Sage version 5.13.beta0, released 2013-10-08
+Sage version 5.13.beta4, released 2013-11-24
diff --git a/build/install b/build/install
@@ -53,6 +53,15 @@ if [ "$SAGE_UPGRADING" = yes ]; then
         export RM="rm -f"
     fi
 
+    # Unset AS and LD if they are set to their default values,
+    # otherwise the AS and LD test from #14296 below will fail.
+    if [ "$AS" = as ]; then
+        unset AS
+    fi
+    if [ "$LD" = ld ]; then
+        unset LD
+    fi
+
     # If we have an old version of sage-location,
     # then manually fix the .la (libtool) files.
     if grep 'lib64' "$SAGE_LOCAL/bin/sage-location" &>/dev/null; then
@@ -252,6 +261,48 @@ else
     fi
 fi
 
+# If we are not installing GCC: check that the assembler and linker
+# used by $CC match $AS and $LD.
+# See http://trac.sagemath.org/sage_trac/ticket/14296
+if [ $need_to_install_gcc != yes ]; then
+    if [ "$AS" != "" ]; then
+        CC_as=`$CC -print-file-name=as 2>/dev/null`
+        CC_as=`command -v $CC_as 2>/dev/null`
+        cmd_AS=`command -v $AS`
+
+        if [ "$CC_as" != "" -a "$CC_as" != "$cmd_AS" ]; then
+            echo >&2 "Error: Mismatch of assemblers between"
+            echo >&2 " * $CC using $CC_as"
+            echo >&2 " * \$AS equal to $AS"
+            if [ "$SAGE_PORT" = "" ]; then
+                echo >&2 "Aborting, either change or unset AS or set SAGE_PORT=yes or set"
+                echo >&2 "SAGE_INSTALL_GCC=yes (this GCC would use assembler $AS)"
+                exit 1
+            else
+                echo >&2 "Continuing since SAGE_PORT is set."
+            fi
+        fi
+    fi
+    if [ "$LD" != "" ]; then
+        CC_ld=`$CC -print-file-name=ld 2>/dev/null`
+        CC_ld=`command -v $CC_ld 2>/dev/null`
+        cmd_LD=`command -v $LD`
+
+        if [ "$CC_ld" != "" -a "$CC_ld" != "$cmd_LD" ]; then
+            echo >&2 "Error: Mismatch of linkers between"
+            echo >&2 " * $CC using $CC_ld"
+            echo >&2 " * \$LD equal to $LD"
+            if [ "$SAGE_PORT" = "" ]; then
+                echo >&2 "Aborting, either change or unset LD or set SAGE_PORT=yes or set"
+                echo >&2 "SAGE_INSTALL_GCC=yes (this GCC would use linker $LD)"
+                exit 1
+            else
+                echo >&2 "Continuing since SAGE_PORT is set."
+            fi
+        fi
+    fi
+fi
+
 ###############################################################################
 # Create the sage_fortran script.
 ###############################################################################

diff --git a/build/pkgs/atlas/SPKG.txt b/build/pkgs/atlas/SPKG.txt
@@ -95,6 +95,11 @@ The package can be configured via three environment variables:
 
 == ChangeLog ==
 
+=== atlas-3.10.1.p6, lapack-3.4.2 (Volker Braun, 11 October 2013) ===
+ * Trac #15270: Do not give up if the upstream shared library build
+   fails
+ * Solaris / ZFS fixes
+
 === atlas-3.10.1.p5, lapack-3.4.2 (Volker Braun, 30 August 2013) ===
  * Trac #15045: Another workaround for shared library bug that does
    not involve static libraries

diff --git a/build/pkgs/atlas/package-version.txt b/build/pkgs/atlas/package-version.txt
@@ -1 +1 @@
-3.10.1.p5
+3.10.1.p6
diff --git a/build/pkgs/atlas/spkg-install b/build/pkgs/atlas/spkg-install
@@ -268,6 +268,7 @@ def configure(arch=None, isa_ext=None):
     print 'Running configure with arch = '+str(arch)+ \
         ', isa extensions '+str(isa_ext), ' thread limit '+str(thread_limit)
     if os.path.isdir(BUILD_DIR):
+        os.chdir(conf['SPKG_DIR'])   # Solaris/ZFS can't delete cwd
         shutil.rmtree(BUILD_DIR)
     os.mkdir(BUILD_DIR)
     os.chdir(BUILD_DIR)
@@ -529,38 +530,39 @@ build_and_save_archdef()
 ######################################################################
 
 rc = make_atlas_library('shared')
-assert_success(rc, bad='Failed to install ATLAS single-threaded shared library',
-               good='Installed ATLAS single-threaded shared library')
+if rc!=0:
+    print 'Failed to build shared library (using the ATLAS build system)'
+else:
+    print 'Installed ATLAS shared library (ATLAS build system)'
 
 rc = make_atlas_library('ptshared')
 if rc!=0:
-    print 'Failed to build threaded library, possibly because your'
-    print 'system does not support it.'
+    print 'Failed to build threaded library (using the ATLAS build system)'
 else:
-    print 'Installed ATLAS multi-threaded shared library'
+    print 'Installed ATLAS multi-threaded shared library (ATLAS build system)'
 
 
 ######################################################################
 ### configure and build atlas and lapack shared library hack
 ######################################################################
 
 rc = configure_shared_library()
-assert_success(rc, bad='Configuring shared ATLAS library failed.',
-               good='Finished configuring shared ATLAS library.')
+assert_success(rc, bad='Configuring shared ATLAS library failed (libtool).',
+               good='Finished configuring shared ATLAS library (libtool).')
 
 have_serial_libs = False
 have_parallel_libs = False
 
 rc = make_shared_library()
 if rc!=0:
     print 'Failed to build serial+parallel shared libraries, possibly because your'
-    print 'system does not support both. Trying to build serial libraries only.'
+    print 'system does not support both. Trying to build serial libraries only (libtool).'
     rc = make_shared_library('all_serial')
     if rc!=0:
-        print 'Failed to build any shared library, installing static library as last resort.'
+        print 'Failed to build any shared library, installing static library as last resort (libtool).'
         INSTALL_STATIC_LIBRARIES = True
     else:
-        print 'Finished building serial shared ATLAS library.'
+        print 'Finished building serial shared ATLAS library (libtool).'
     have_serial_libs = True
 else:
     have_parallel_libs = True
@@ -572,13 +574,13 @@ else:
 
 if have_parallel_libs:
     rc = make_shared_library('install')
-    assert_success(rc, bad='Installing the parallel+serial shared ATLAS library failed.',
-                   good='Finished installing parallel+serial shared ATLAS library.')
+    assert_success(rc, bad='Installing the parallel+serial shared ATLAS library failed (libtool).',
+                   good='Finished installing parallel+serial shared ATLAS library (libtool).')
 
 if have_serial_libs:
     rc = make_shared_library('install_serial')
-    assert_success(rc, bad='Installing the serial shared ATLAS library failed.',
-                   good='Finished installing serial shared ATLAS library.')
+    assert_success(rc, bad='Installing the serial shared ATLAS library failed (libtool).',
+                   good='Finished installing serial shared ATLAS library (libtool).')
 
 
 ######################################################################

diff --git a/build/pkgs/boehm_gc/SPKG.txt b/build/pkgs/boehm_gc/SPKG.txt
@@ -6,11 +6,7 @@ The Boehm-Demers-Weiser conservative garbage collector.
 
 == License ==
 
-Permissive BSD + GPL 2.0+
-
-== SPKG Maintainers ==
-
-  * William Stein
+* Permissive BSD + GPL 2.0+
 
 == Upstream Contact ==
 
@@ -23,10 +19,17 @@ None.
 
 == Special Update/Build Instructions ==
 
-None. Sources in src are vanilla.
+=== Patches ===
+ * cygwin64.patch: let libgc build on Cygwin64.
 
 == Changelog ==
 
+=== boehm_gc-7.2d.p0 (Jean-Pierre Flori, 11 June 2013) ===
+ * #14710: Update to version 7.2d.
+ * Remove patches integrated upstream.
+ * Add cygwin64.patch from Cygwin64 libgc package to let it build
+   on Cygwin64.
+
 === boehm_gc-7.2.alpha6.p2 (Simon King, Dec 10 2011) ===
  * #12131: Use --libdir, to make the package work on openSUSE
 
@@ -78,4 +81,3 @@ None. Sources in src are vanilla.
 
 === boehm_gc-7.1 (Gary Furnish) ===
  * Initial version
-
diff --git a/build/pkgs/boehm_gc/checksums.ini b/build/pkgs/boehm_gc/checksums.ini
@@ -1,3 +1,3 @@
-sha1=d2b73db75ea173ebd07a3ee04b4cd91e1af81eaf
-md5=1eee767e11296fb1b7d11d273fe072c7
-cksum=2375122679
+sha1=4013e5d6b685e1a3c7ff9b5447405a2b452731be
+md5=48232de5b36573da6415ece66a9b9084
+cksum=2689595432
diff --git a/build/pkgs/boehm_gc/package-version.txt b/build/pkgs/boehm_gc/package-version.txt
@@ -1 +1 @@
-7.2.alpha6.p2
+7.2d.p0
diff --git a/build/pkgs/boehm_gc/patches/cygwin64.patch b/build/pkgs/boehm_gc/patches/cygwin64.patch
@@ -0,0 +1,104 @@
+--- a/include/gc.h	2012-08-09 16:25:13.000000000 -0400
++++ b/include/gc.h	2013-04-22 13:10:01.101686000 -0400
+@@ -1385,7 +1385,14 @@
+ /* THREAD_LOCAL_ALLOC defined and the initial allocation call is not    */
+ /* to GC_malloc() or GC_malloc_atomic().                                */
+
+-#ifdef __CYGWIN32__
++#ifdef __CYGWIN__
++#ifdef __x86_64__
++  extern int __data_start__[], __data_end__[], __bss_start__[], __bss_end__[];
++#define GC_DATASTART (__data_start__ < __bss_start__ ?\
++                      (void *)__data_start__ : (void *)__bss_start__)
++#define GC_DATAEND (__data_end__ < __bss_end__ ?\
++                      (void *)__data_end__ : (void *)__bss_end__)
++#else
+   /* Similarly gnu-win32 DLLs need explicit initialization from the     */
+   /* main program, as does AIX.                                         */
+   extern int _data_start__[], _data_end__[], _bss_start__[], _bss_end__[];
+@@ -1393,6 +1400,7 @@
+                        (void *)_data_start__ : (void *)_bss_start__)
+ # define GC_DATAEND (_data_end__ > _bss_end__ ? \
+                      (void *)_data_end__ : (void *)_bss_end__)
++#endif
+ # define GC_INIT_CONF_ROOTS GC_add_roots(GC_DATASTART, GC_DATAEND); \
+                                  GC_gcollect() /* For blacklisting. */
+         /* Required at least if GC is in a DLL.  And doesn't hurt. */
+--- a/include/private/gcconfig.h	2012-08-09 16:25:13.000000000 -0400
++++ b/include/private/gcconfig.h	2013-04-21 12:52:28.024399600 -0400
+@@ -432,10 +432,20 @@
+ #   endif
+ #   define mach_type_known
+ # endif
+-# if defined(__CYGWIN32__) || defined(__CYGWIN__)
++# if defined(__CYGWIN32__)
+ #   define I386
+ #   define CYGWIN32
+ #   define mach_type_known
++#if defined(__CYGWIN__)
++#  if defined(__LP64__)
++#    define X86_64
++#    define mach_type_known
++#  else
++#    define I386
++#  endif
++#  define CYGWIN32
++#  define mach_type_known
++#endif
+ # endif
+ # if defined(__MINGW32__) && !defined(mach_type_known)
+ #   define I386
+@@ -502,6 +512,16 @@
+ #    define mach_type_known
+ # endif
+
++#if defined(__CYGWIN__)
++#  if defined(__LP64__)
++#    define X86_64
++#    define mach_type_known
++#  else
++#    define I386
++#  endif
++#  define CYGWIN32
++#  define mach_type_known
++#endif
+ /* Feel free to add more clauses here */
+
+ /* Or manually define the machine type here.  A machine type is         */
+@@ -2259,6 +2279,19 @@
+ #       define GWW_VDB
+ #       define DATAEND  /* not needed */
+ #   endif
++
++#   ifdef CYGWIN32
++#       define OS_TYPE "CYGWIN32"
++#       define DATASTART ((ptr_t)GC_DATASTART)  /* From gc.h */
++#       define DATAEND   ((ptr_t)GC_DATAEND)
++#       define ALIGNMENT 8
++#       undef STACK_GRAN
++#       define STACK_GRAN 0x10000
++#       ifdef USE_MMAP
++#         define NEED_FIND_LIMIT
++#         define USE_MMAP_ANON
++#       endif
++#   endif
+ # endif /* X86_64 */
+
+ # ifdef HEXAGON
+--- a/os_dep.c	2012-08-09 16:25:13.000000000 -0400
++++ b/os_dep.c	2013-04-22 12:43:32.202498600 -0400
+@@ -770,7 +770,14 @@
+     /* gcc version of boehm-gc).                                        */
+     GC_API int GC_CALL GC_get_stack_base(struct GC_stack_base *sb)
+     {
++# ifdef __x86_64__
++      PNT_TIB pTib = NtCurrentTeb();
++      void * _tlsbase = pTib->StackBase;
++      /*void * _tlsbase = NtCurrentTeb()->pTib.StackBase;*/
++      /*extern void * _tlsbase __asm__ ("%gs:8");*/
++# else
+       extern void * _tlsbase __asm__ ("%fs:4");
++# endif
+       sb -> mem_base = _tlsbase;
+       return GC_SUCCESS;
+     }