Merge branch 'develop' into t/2516/ticket/2516

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta7, released 2014-04-08
+Sage version 6.2.beta8, released 2014-04-14

build/pkgs/atlas/spkg-install

@@ -313,10 +313,13 @@ def configure(arch=None, isa_ext=None):
         if conf['Darwin?']:
             atlas_osnam = 'OSX'
         elif conf['CYGWIN?']:
-            if conf['64bit?']:
-                atlas_osnam = 'Win64'
-            else:
-                atlas_osnam = 'WinNT'
+# Picking Win64 currently does not work on Cygwin though it might be a better
+# choice in the future.
+# Not that ATLAS does not seem to officialy support Cygwin64 anyway in 3.10.1.
+#            if conf['64bit?']:
+#                atlas_osnam = 'Win64'
+#            else:
+            atlas_osnam = 'WinNT'
         else:
             atlas_osnam = conf['system']
         atlas_system = ATLAS_OSTYPE.index(atlas_osnam)

build/pkgs/bzip2/SPKG.txt

@@ -28,11 +28,9 @@ None
 == Special Update/Build Instructions ==
 
 This package must not be bzip2 compressed, so create it using
-
 tar c bzip2-1.0.6 | gzip --best >bzip2-1.0.6.spkg
 
-== Changelog ==
+The build system has been autotoolized based on a patch by the Suse folk at
+http://ftp.uni-kl.de/pub/linux/suse/people/sbrabec/bzip2/for_downstream/bzip2-1.0.6-autoconfiscated.patch
 
-=== bzip2-1.0.6 (Jeroen Demeyer, 5 March 2012) ===
- * Trac #12102: initial version as "standard" package.  Adapted
-   spkg-install from the old spkg/base/bzip2-1.0.5-install.
+See patches/autotools and spkg-src for details.

build/pkgs/bzip2/checksums.ini

@@ -1,4 +1,4 @@
 tarball=bzip2-VERSION.tar.gz
-sha1=06cd2d25c80bea77582cacc9ea33a5cd1756c74a
-md5=a4e60f6889aa9cb752b15ed64ebbb7f8
-cksum=2233929913
+sha1=3533f6a2325e4e727a2c8ead5ea48202e9b9b423
+md5=df2f60f9a3d5f6da51bf313d060ba5e1
+cksum=1584769449

build/pkgs/bzip2/package-version.txt

@@ -1 +1 @@
-1.0.6
+1.0.6.20140317

build/pkgs/bzip2/patches/autotools/Makefile.am

@@ -0,0 +1,138 @@
+lib_LTLIBRARIES = libbz2.la
+
+libbz2_la_SOURCES = \
+	blocksort.c \
+	huffman.c \
+	crctable.c \
+	randtable.c \
+	compress.c \
+	decompress.c \
+	bzlib.c
+
+libbz2_la_LDFLAGS = \
+	-version-info $(BZIP2_LT_CURRENT):$(BZIP2_LT_REVISION):$(BZIP2_LT_AGE) \
+	-no-undefined
+
+include_HEADERS = bzlib.h
+
+noinst_HEADERS = bzlib_private.h
+
+bin_PROGRAMS = bzip2 bzip2recover
+
+bzip2_SOURCES = bzip2.c
+bzip2_LDADD = libbz2.la
+
+bzip2recover_SOURCES = bzip2recover.c
+bzip2recover_LDADD = libbz2.la
+
+bin_SCRIPTS = bzgrep bzmore bzdiff
+
+man_MANS = bzip2.1 bzgrep.1 bzmore.1 bzdiff.1
+
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = bzip2.pc
+
+$(pkgconfig_DATA): $(srcdir)/bzip2.pc.in config.status
+
+install-exec-hook:
+	rm -f $(DESTDIR)$(bindir)/`echo "bunzip2" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzcat" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzegrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzfgrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzless" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzcmp" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzip2" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bunzip2" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzip2" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bzcat" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzgrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bzegrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzgrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bzfgrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzmore" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bzless" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	$(LN_S) `echo "bzdiff" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'` $(DESTDIR)$(bindir)/`echo "bzcmp" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+
+install-data-hook:
+	echo ".so man1/`echo "bzip2" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bunzip2" | sed 's,^.*/,,;$(transform)'`.1
+	echo ".so man1/`echo "bzip2" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bzcat" | sed 's,^.*/,,;$(transform)'`.1
+	echo ".so man1/`echo "bzgrep" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bzegrep" | sed 's,^.*/,,;$(transform)'`.1
+	echo ".so man1/`echo "bzgrep" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bzfgrep" | sed 's,^.*/,,;$(transform)'`.1
+	echo ".so man1/`echo "bzmore" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bzless" | sed 's,^.*/,,;$(transform)'`.1
+	echo ".so man1/`echo "bzdiff" | sed 's,^.*/,,;$(transform)'`.1" >$(DESTDIR)$(mandir)/man1/`echo "bzcmp" | sed 's,^.*/,,;$(transform)'`.1
+
+uninstall-hook:
+	rm -f $(DESTDIR)$(bindir)/`echo "bunzip2" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzcat" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzegrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzfgrep" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzless" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(bindir)/`echo "bzcmp" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bunzip2" | sed 's,^.*/,,;$(transform)'`.1
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bzcat" | sed 's,^.*/,,;$(transform)'`.1
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bzegrep" | sed 's,^.*/,,;$(transform)'`.1
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bzfgrep" | sed 's,^.*/,,;$(transform)'`.1
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bzless" | sed 's,^.*/,,;$(transform)'`.1
+	rm -f $(DESTDIR)$(mandir)/man1/`echo "bzcmp" | sed 's,^.*/,,;$(transform)'`.1
+
+test: bzip2
+	@cat $(srcdir)/words1
+	./bzip2 -1  <$(srcdir)/sample1.ref >sample1.rb2
+	./bzip2 -2  <$(srcdir)/sample2.ref >sample2.rb2
+	./bzip2 -3  <$(srcdir)/sample3.ref >sample3.rb2
+	./bzip2 -d  <$(srcdir)/sample1.bz2 >sample1.tst
+	./bzip2 -d  <$(srcdir)/sample2.bz2 >sample2.tst
+	./bzip2 -ds <$(srcdir)/sample3.bz2 >sample3.tst
+	cmp $(srcdir)/sample1.bz2 sample1.rb2
+	cmp $(srcdir)/sample2.bz2 sample2.rb2
+	cmp $(srcdir)/sample3.bz2 sample3.rb2
+	cmp sample1.tst $(srcdir)/sample1.ref
+	cmp sample2.tst $(srcdir)/sample2.ref
+	cmp sample3.tst $(srcdir)/sample3.ref
+	@cat $(srcdir)/words3
+
+manual: $(srcdir)/manual.html $(srcdir)/manual.ps $(srcdir)/manual.pdf
+
+manual.ps: $(MANUAL_SRCS)
+	cd $(srcdir); ./xmlproc.sh -ps manual.xml
+
+manual.pdf: $(MANUAL_SRCS)
+	cd $(srcdir); ./xmlproc.sh -pdf manual.xml
+
+manual.html: $(MANUAL_SRCS)
+	cd $(srcdir); ./xmlproc.sh -html manual.xml
+
+EXTRA_DIST = \
+	$(bin_SCRIPTS) \
+	$(man_MANS) \
+	README.autotools \
+	README.XML.STUFF \
+	bz-common.xsl \
+	bz-fo.xsl \
+	bz-html.xsl \
+	bzip.css \
+	bzip2.1.preformatted \
+	bzip2.pc.in \
+	bzip2.txt \
+	dlltest.c \
+	dlltest.dsp \
+	entities.xml \
+	format.pl \
+	libbz2.def \
+	libbz2.dsp \
+	makefile.msc \
+	manual.html \
+	manual.pdf \
+	manual.ps \
+	manual.xml \
+	mk251.c \
+	sample1.bz2 \
+	sample1.ref \
+	sample2.bz2 \
+	sample2.ref \
+	sample3.bz2 \
+	sample3.ref \
+	spewG.c \
+	unzcrash.c \
+	words0 \
+	words1 \
+	words2 \
+	words3 \
+	xmlproc.sh
+
+ACLOCAL_AMFLAGS = -I m4

build/pkgs/bzip2/patches/autotools/README.autotools

@@ -0,0 +1,39 @@
+bzip2 autoconfiscated
+=====================
+
+Temporarily at http://ftp.suse.com/pub/people/sbrabec/bzip2/ expecting
+that it will become a new upstream version to prevent per-distribution
+shared library patching done by nearly each Linux vendor separately.
+
+Autoconfiscation brings standard ./configure ; make ; make install
+installation, seamless support of DESTDIR, automatic check for supported
+CFLAGS, standard shared library support, automatic large files CFLAGS
+check and all things that are supported by automake.
+
+It makes obsolete Makefile-libbz2_so and README.COMPILATION.PROBLEMS.
+Now configure should automatically detect correct build flags.
+
+In case of any problem or question with autotools support feel free to
+contact me: Stanislav Brabec <sbrabec@suse.cz>
+
+Autoconfiscated version binaries are exactly equal to
+bzip2-1.0.5.tar.gz. There are only few changes. See below.
+
+
+New features:
+
+Trivial link man pages for bzcat and bunzip2 added.
+
+bzip2.pc file for pkg-config. Packages can use it for checks.
+
+
+Incompatible changes:
+
+soname change. Libtool has no support for two parts soname suffix (e. g.
+libbz2.so.1.0). It must be a single number (e. g. libbz2.so.1). That is
+why soname must change. But I see not a big problem with it. Several
+distributions already use the new number instead of the non-standard
+number from Makefile-libbz2_so.
+
+To be super-safe, I incremented minor number of the library file, so
+both instances of the shared library can live together.

build/pkgs/bzip2/patches/autotools/bzip2.pc.in

@@ -0,0 +1,11 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+bindir=@bindir@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: bzip2
+Description: Lossless, block-sorting data compression
+Version: @VERSION@
+Libs: -L${libdir} -lbz2
+Cflags: -I${includedir}

build/pkgs/bzip2/patches/autotools/configure.ac

@@ -0,0 +1,70 @@
+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.57])
+AC_INIT([bzip2], [1.0.6], [Julian Seward <jseward@bzip.org>])
+BZIP2_LT_CURRENT=1
+BZIP2_LT_REVISION=6
+BZIP2_LT_AGE=0
+AC_CONFIG_SRCDIR([bzlib.h])
+AC_CONFIG_MACRO_DIR([m4])
+
+AM_INIT_AUTOMAKE
+AM_MAINTAINER_MODE
+
+# Checks for programs.
+AC_PROG_AWK
+AC_PROG_CC
+AC_PROG_INSTALL
+AC_PROG_LN_S
+AC_PROG_MAKE_SET
+LT_INIT([win32-dll])
+PKG_PROG_PKG_CONFIG
+
+# Checks for libraries.
+
+# Checks for header files.
+
+# Checks for typedefs, structures, and compiler characteristics.
+
+# Check for system features.
+AC_SYS_LARGEFILE
+
+AC_MSG_CHECKING([whether compiler understands -Wall])
+save_CFLAGS="$CFLAGS"
+CFLAGS="$CFLAGS -Wall"
+AC_TRY_COMPILE([], [], [
+	AC_MSG_RESULT([yes])
+], [
+	AC_MSG_RESULT([no])
+	CFLAGS="$save_CFLAGS"
+])
+
+AC_MSG_CHECKING([whether compiler understands -Winline])
+save_CFLAGS="$CFLAGS"
+CFLAGS="$CFLAGS -Winline"
+AC_TRY_COMPILE([], [], [
+	AC_MSG_RESULT([yes])
+], [
+	AC_MSG_RESULT([no])
+	CFLAGS="$save_CFLAGS"
+])
+
+AC_MSG_CHECKING([whether compiler understands -fno-strength-reduce])
+save_CFLAGS="$CFLAGS"
+CFLAGS="$CFLAGS -fno-strength-reduce"
+AC_TRY_COMPILE([], [], [
+	AC_MSG_RESULT([yes])
+], [
+	AC_MSG_RESULT([no])
+	CFLAGS="$save_CFLAGS"
+])
+
+# Checks for library functions.
+
+# Write the output.
+AC_SUBST([BZIP2_LT_CURRENT])
+AC_SUBST([BZIP2_LT_REVISION])
+AC_SUBST([BZIP2_LT_AGE])
+AC_CONFIG_FILES([Makefile bzip2.pc])
+AC_OUTPUT

build/pkgs/bzip2/spkg-install

@@ -15,31 +15,37 @@ if [ "x$SAGE64" = xyes ]; then
     CFLAGS="$CFLAG64 $CFLAGS"
 fi
 
-export CFLAGS="-fPIC -O2 -g $CFLAGS"
+export CFLAGS="-O2 -g $CFLAGS"
 
-cd src
+cd src/src
 
-########################################################################
-# Build bzip2
-########################################################################
+# Patch bzip2
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
 
-# Since bzip2 doesn't use configure, we need to pass flags as arguments
-# to make.
-$MAKE CC="$CC" CFLAGS="$CFLAGS"
+# Autotoolify bzip2
+cp -r -f ../autotools/* ./
+
+./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"
+if [ $? -ne 0 ]; then
+    echo >&2 "Error configuring bzip2"
+    exit 1
+fi
+
+$MAKE
 if [ $? -ne 0 ]; then
     echo >&2 "Error building bzip2"
     exit 1
 fi
 
-$MAKE install PREFIX="$SAGE_LOCAL" CC="$CC" CFLAGS="$CFLAGS"
+$MAKE install
 if [ $? -ne 0 ]; then
     echo >&2 "Error installing bzip2"
     exit 1
 fi
-
-# Fix a bunch of hard-coding that bzip2 does during installation.
-cd "$SAGE_LOCAL/bin"
-rm bzcmp; ln -s bzdiff bzcmp
-rm bzegrep; ln -s bzgrep bzegrep
-rm bzfgrep; ln -s bzgrep bzfgrep
-rm bzless; ln -s bzmore bzless

build/pkgs/bzip2/spkg-src

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+BZIP2=bzip2-1.0.6
+
+set -e
+shopt -s extglob
+
+# Remove old sources and download new
+rm -rf src
+mkdir src
+cd src
+
+tar xzf <( curl -L "http://www.bzip.org/1.0.6/$BZIP2.tar.gz" )
+
+if [ ! -d "$BZIP2" ]; then
+    echo "$BZIP2 directory not in tarball, aborting"
+    exit 1
+fi
+mv "$BZIP2" src
+
+# Autotoolify
+cp -a ../patches/autotools ./
+cd autotools
+mkdir m4
+touch NEWS README AUTHORS ChangeLog
+autoreconf -fiv
+rm -rf autom4te.cache

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=fd8b009ba519b4574501dfb91f24eaa1f667a84e
-md5=3d4a0effe4e963b61b52db56e329b1c3
-cksum=3975517455
+sha1=1bc0c5bed6782f0b4178509b5a2f71803e974660
+md5=edbfd3a7fe2451b2ea8aa926cd1bb249
+cksum=1897111074