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2.11.0

This commit is contained in:
Tom Callaway 2010-04-22 21:56:33 +00:00
parent 21eaf582af
commit 36e39e36d0
10 changed files with 19 additions and 10388 deletions
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2
.cvsignore
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@ -1 +1 @@
R-2.10.1.tar.gz
R-2.11.0.tar.gz

64
R-2.1.0-gcc4.patch
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@ -1,64 +0,0 @@
--- R-2.0.1/src/main/connections.c.BAD 2005-03-24 16:59:46.000000000 -0600
+++ R-2.0.1/src/main/connections.c 2005-03-24 16:56:22.000000000 -0600
@@ -2194,7 +2194,7 @@
va_list(ap);
va_start(ap, format);
- res = con->vfprintf(con, format, ap);
+ res = (con->vfprintf)(con, format, ap);
va_end(ap);
return res;
}
@@ -2292,7 +2292,7 @@
{
va_list(ap);
va_start(ap, format);
- con->vfprintf(con, format, ap);
+ (con->vfprintf)(con, format, ap);
va_end(ap);
}
--- R-2.0.1/src/main/printutils.c.BAD 2005-03-24 16:58:59.000000000 -0600
+++ R-2.0.1/src/main/printutils.c 2005-03-24 16:59:12.000000000 -0600
@@ -427,7 +427,7 @@
do{
con = getConnection(con_num);
- con->vfprintf(con, format, arg);
+ (con->vfprintf)(con, format, arg);
con->fflush(con);
con_num = getActiveSink(i++);
} while(con_num>0);
@@ -452,7 +452,7 @@
/* should never happen, but in case of corruption... */
R_ErrorCon = 2;
} else {
- con->vfprintf(con, format, arg);
+ (con->vfprintf)(con, format, arg);
con->fflush(con);
return;
}
--- R-2.0.1/src/include/R_ext/RS.h.BAD 2005-03-25 07:59:09.000000000 -0600
+++ R-2.0.1/src/include/R_ext/RS.h 2005-03-25 07:59:26.000000000 -0600
@@ -34,8 +34,8 @@
#ifndef STRICT_R_HEADERS
#define R_PROBLEM_BUFSIZE 4096
-#define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];sprintf(R_problem_buf,
-#define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];sprintf(R_problem_buf,
+#define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
+#define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
#define ERROR ),error(R_problem_buf);}
#define RECOVER(x) ),error(R_problem_buf);}
#define WARNING(x) ),warning(R_problem_buf);}
--- R-2.1.0/src/main/scan.c.BAD 2005-04-18 09:00:40.000000000 -0500
+++ R-2.1.0/src/main/scan.c 2005-04-18 09:00:56.000000000 -0500
@@ -1638,7 +1638,7 @@
{
va_list(ap);
va_start(ap, format);
- con->vfprintf(con, format, ap);
+ (con->vfprintf)(con, format, ap);
va_end(ap);
}

10076
R-2.4.0-patched-2006-11-03.patch
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File diff suppressed because it is too large Load Diff

149
R-2.5.0-pkgconfig.patch
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@ -1,149 +0,0 @@
diff -uNr R-2.5.0/src/nmath/standalone/Makefile.in R-2.5.0-patched/src/nmath/standalone/Makefile.in
--- R-2.5.0/src/nmath/standalone/Makefile.in 2007-03-26 18:42:08.000000000 +0200
+++ R-2.5.0-patched/src/nmath/standalone/Makefile.in 2007-04-29 14:50:55.000000000 +0200
@@ -67,7 +67,7 @@
libRmath_la_LDFLAGS =
CLEANFILES = Makedeps *.d *.o *.lo test $(SOURCES)
-DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
+DISTCLEANFILES = Makefile libRmath.pc $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
DEFS = -DHAVE_CONFIG_H -DMATHLIB_STANDALONE
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) -I$(srcdir)/.. $(CPPFLAGS) $(DEFS)
@@ -78,7 +78,7 @@
@r_cc_lo_rules_frag@
-all: Makefile inc static shared
+all: Makefile inc static shared build-pc
inc:
(cd ../../include; $(MAKE) Rmath.h)
@@ -100,6 +100,11 @@
shared: Makefile ../../include/Rconfig.h Copy Makedeps
@$(MAKE) $(Rexeclibdir_LTLIBRARIES)
+build-pc:
+ @$(SED) -e "s:@libdir:$(libdir):" -e "s:@includedir:$(includedir):" \
+ -e 's/@VERSION/$(VERSION)/' -e 's/@libm/$(LIBM)/' $(srcdir)/libRmath.pc.in \
+ > "libRmath.pc"
+
../../include/Rconfig.h:
(cd $(@D); $(MAKE) $(@F))
@@ -163,9 +168,7 @@
install-pc:
@$(MKINSTALLDIRS) "$(libdir)/pkgconfig"
- @$(SED) -e "s:@libdir:$(libdir):" -e "s:@includedir:$(includedir):" \
- -e 's/@VERSION/$(VERSION)/' -e 's/@libm/$(LIBM)/' $(srcdir)/libRmath.pc.in \
- > "$(libdir)/pkgconfig/libRmath.pc"
+ @$(INSTALL_DATA) libRmath.pc "$(libdir)/pkgconfig/libRmath.pc"
uninstall:
@rm -f $(includedir)/Rmath.h $(libdir)/$(libRmath_la) $(libdir)/libRmath.a "$(libdir)/pkgconfig/libRmath.pc"
diff -uNr R-2.5.0/src/scripts/Makefile.in R-2.5.0-patched/src/scripts/Makefile.in
--- R-2.5.0/src/scripts/Makefile.in 2007-03-26 18:42:09.000000000 +0200
+++ R-2.5.0-patched/src/scripts/Makefile.in 2007-04-29 14:50:14.000000000 +0200
@@ -23,17 +23,22 @@
DISTFILES = Makefile.in Makefile.win $(SCRIPTS_S) $(SCRIPTS_B_IN) R.sh.in
CLEANFILES =
-DISTCLEANFILES = Makefile R.fe R.sh $(SCRIPTS_B)
+DISTCLEANFILES = Makefile R.fe R.fe2 R.sh $(SCRIPTS_B)
all: Makefile R
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
-R: $(SCRIPTS_B) R.fe
+R: $(SCRIPTS_B) R.fe R.fe2
@$(MAKE) rhome=$(top_builddir) install-cmds
@$(INSTALL_SCRIPT) R.fe $(top_builddir)/bin/R
+R.fe2:
+ @(d=`echo '$(rhome)' | sed 's,/,\\\/,g';`; \
+ sed -e "s/\\(R_HOME_DIR=\\).*/\\1$${d}/;" -e "s+\\(R_SHARE_DIR=\\).*+\\1$(rsharedir)+;" -e "s+\\(R_INCLUDE_DIR=\\).*+\\1$(rincludedir)+;" -e "s+\\(R_DOC_DIR=\\).*+\\1$(rdocdir)+;"\
+ < R.fe > $@)
+
## <NOTE>
## Seems we need target rules for creating FOO from FOO.in: pattern
## rules ('%:%.in') are not portable, and some versions of Make do not
@@ -95,10 +100,8 @@
install: installdirs install-cmds
@rm -f $(bindir)/R
- @(d=`echo '$(rhome)' | sed 's,/,\\\/,g';`; \
- sed -e "s/\\(R_HOME_DIR=\\).*/\\1$${d}/;" -e "s+\\(R_SHARE_DIR=\\).*+\\1$(rsharedir)+;" -e "s+\\(R_INCLUDE_DIR=\\).*+\\1$(rincludedir)+;" -e "s+\\(R_DOC_DIR=\\).*+\\1$(rdocdir)+;"\
- < R.fe > "$(Rexecbindir)/R")
- @$(INSTALL_SCRIPT) "$(Rexecbindir)/R" "$(bindir)/R"
+ @$(INSTALL_SCRIPT) R.fe2 "$(Rexecbindir)/R"
+ @$(INSTALL_SCRIPT) R.fe2 "$(bindir)/R"
@chmod 755 "$(bindir)/R" "$(Rexecbindir)/R"
## why of all the scriots does this alone chmod just one copy?
installdirs:
diff -uNr R-2.5.0/src/unix/Makefile.in R-2.5.0-patched/src/unix/Makefile.in
--- R-2.5.0/src/unix/Makefile.in 2007-03-26 18:41:33.000000000 +0200
+++ R-2.5.0-patched/src/unix/Makefile.in 2007-04-29 14:51:55.000000000 +0200
@@ -26,7 +26,7 @@
@WANT_R_SHLIB_TRUE@ALL_CFLAGS = $(ALL_CFLAGS_LO)
-all: Makefile Makedeps R
+all: Makefile Makedeps R
Makefile: $(srcdir)/Makefile.in \
$(top_builddir)/config.status \
@@ -38,11 +38,23 @@
@cat $(DEPENDS) >> Makefile
@touch $@
-R: Makefile
+R: Makefile
@$(MAKE) Makedeps
@WANT_R_SHLIB_FALSE@ @$(MAKE) libunix.a
@WANT_R_SHLIB_TRUE@ @$(MAKE) stamp-lo
+ @$(MAKE) rhome=$(abs_top_builddir) build-Rscript
@$(MAKE) rhome=$(abs_top_builddir) install-Rscript
+ @$(MAKE) build-Rscript
+ @$(MAKE) build-pc
+
+build-pc:
+ @$(SED) -e "s:@rhome:$(rhome):" -e "s:@rincludedir:$(rincludedir):" \
+ -e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \
+ > "libR.pc"
+
+build-Rscript:
+ $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"$(rhome)"' -o Rscript \
+ $(srcdir)/Rscript.c
## is this portable?
../include/Rversion.h:
@@ -60,22 +72,19 @@
clean:
@-rm -rf .libs _libs
@-rm -f Makedeps *.d *.o *.a *.lo *.la stamp-lo
+ @-rm -f Rscript libR.pc
distclean: clean
@-rm -f Makefile
maintainer-clean: distclean
-## we need to build at install time to capture the correct 'rhome'
+## install previously built Rscript
install-Rscript:
- $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"$(rhome)"' -o Rscript \
- $(srcdir)/Rscript.c
@$(MKINSTALLDIRS) "$(Rexecbindir)"
@$(INSTALL_PROGRAM) Rscript "$(Rexecbindir)/Rscript"
-## substitute at install time to allow 'prefix' to be overridden
+## install previously built libR.pc
install-pc:
@$(MKINSTALLDIRS) "$(libdir)/pkgconfig"
- @$(SED) -e "s:@rhome:$(rhome):" -e "s:@rincludedir:$(rincludedir):" \
- -e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \
- > "$(libdir)/pkgconfig/libR.pc"
+ @$(INSTALL_DATA) libR.pc "$(libdir)/pkgconfig/libR.pc"
install: install-Rscript @WANT_R_SHLIB_TRUE@ install-pc
@$(MKINSTALLDIRS) "$(bindir)"
@$(INSTALL_PROGRAM) Rscript "$(bindir)/Rscript"

18
R-2.7.0-bad-path.patch
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@ -1,18 +0,0 @@
Index: src/unix/Makefile.in
===================================================================
--- src/unix/Makefile.in (revision 45534)
+++ src/unix/Makefile.in (revision 45535)
@@ -78,11 +78,11 @@
-e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \
> "$(DESTDIR)$(libdir)/pkgconfig/libR.pc"
-install: install-main install-Rscript
+install: install-main
install: @WANT_R_SHLIB_TRUE@ install-pc
install: @WANT_R_STATIC_TRUE@ install-pc
-install-main:
+install-main: install-Rscript
@$(MKINSTALLDIRS) "$(DESTDIR)$(bindir)"
@$(INSTALL_PROGRAM) Rscript "$(DESTDIR)$(bindir)/Rscript"

27
R-2.7.1-javareconf-tmpfix.patch
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@ -1,27 +0,0 @@
diff -up R-2.7.1/src/scripts/javareconf.BAD R-2.7.1/src/scripts/javareconf
--- R-2.7.1/src/scripts/javareconf.BAD 2008-08-29 11:04:21.000000000 -0400
+++ R-2.7.1/src/scripts/javareconf 2008-08-29 11:05:34.000000000 -0400
@@ -125,16 +125,17 @@ fi
javac_works='not present'
if test -n "$JAVAC"; then
javac_works='not functional'
- rm -rf /tmp/A.java /tmp/A.class
- echo "public class A { }" > /tmp/A.java
- if test -e /tmp/A.java; then
- if "${JAVAC}" /tmp/A.java >/dev/null; then
- if test -e /tmp/A.class; then
+ tempdir=`mktemp -d`
+ echo "public class A { }" > ${tempdir}/A.java
+ if test -e ${tempdir}/A.java; then
+ if "${JAVAC}" ${tempdir}/A.java >/dev/null; then
+ if test -e ${tempdir}/A.class; then
javac_works=yes
fi
fi
fi
- rm -rf /tmp/A.java /tmp/A.class
+ rm -rf ${tempdir}
+
fi
if test "${javac_works}" = yes; then
echo "Java compiler : ${JAVAC}"

26
R-2.8.0-HAVE_BZLIB_H.patch
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@ -1,26 +0,0 @@
diff -up R-2.8.0/configure.BAD R-2.8.0/configure
--- R-2.8.0/configure.BAD 2008-10-26 11:51:56.000000000 -0400
+++ R-2.8.0/configure 2008-10-26 11:52:31.000000000 -0400
@@ -44779,6 +44779,11 @@ else
have_bzlib=no
fi
if test "x${have_bzlib}" = xyes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BZLIB_H 1
+_ACEOF
+
{ echo "$as_me:$LINENO: checking if bzip2 version >= 1.0.5" >&5
echo $ECHO_N "checking if bzip2 version >= 1.0.5... $ECHO_C" >&6; }
if test "${r_cv_have_bzlib+set}" = set; then
diff -up R-2.8.0/m4/R.m4.BAD R-2.8.0/m4/R.m4
--- R-2.8.0/m4/R.m4.BAD 2008-09-21 18:05:06.000000000 -0400
+++ R-2.8.0/m4/R.m4 2008-10-26 11:53:05.000000000 -0400
@@ -3055,6 +3055,7 @@ else
have_bzlib=no
fi
if test "x${have_bzlib}" = xyes; then
+AC_DEFINE(HAVE_BZLIB_H, 1, [Define to 1 if you have bzlib.h.])
AC_CACHE_CHECK([if bzip2 version >= 1.0.5], [r_cv_have_bzlib],
[AC_LANG_PUSH(C)
r_save_LIBS="${LIBS}"

10
R-LANG.patch
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@ -1,10 +0,0 @@
--- R-1.9.0/src/scripts/R.sh.in 2004-03-07 12:15:11.000000000 +0100
+++ R-1.9.0-fixed/src/scripts/R.sh.in 2004-04-01 18:43:49.000000000 +0200
@@ -1,6 +1,7 @@
#!/bin/sh
# Shell wrapper for R executable.
+LANG=C
R_HOME_DIR=
if test -n "${R_HOME}" && \
test "${R_HOME}" != "${R_HOME_DIR}"; then

33
R.spec
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@ -5,14 +5,13 @@
%endif
Name: R
Version: 2.10.1
Release: 2%{?dist}
Version: 2.11.0
Release: 1%{?dist}
Summary: A language for data analysis and graphics
URL: http://www.r-project.org
Source0: ftp://cran.r-project.org/pub/R/src/base/R-2/R-%{version}.tar.gz
Source1: macros.R
Source2: R-make-search-index.sh
Patch1: R-2.7.2-filter_asoption.patch
License: GPLv2+
Group: Applications/Engineering
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
@ -57,34 +56,33 @@ Requires: perl, sed, gawk, texlive-latex, texlive-dvips, less, vi
# depend on one of these submodules rather than just R. These are provided for
# packager convenience.
Provides: R-base = %{version}
Provides: R-boot = 1.2.41
Provides: R-class = 7.3.1
Provides: R-cluster = 1.12.1
Provides: R-boot = 1.2.42
Provides: R-class = 7.3.2
Provides: R-cluster = 1.12.3
Provides: R-codetools = 0.2.2
Provides: R-datasets = %{version}
Provides: R-foreign = 0.8.38
Provides: R-foreign = 0.8.40
Provides: R-graphics = %{version}
Provides: R-grDevices = %{version}
Provides: R-grid = %{version}
Provides: R-KernSmooth = 2.23.3
Provides: R-lattice = 0.17.26
Provides: R-MASS = 7.3.4
Provides: R-Matrix = 0.999375.33
Provides: R-lattice = 0.18.5
Provides: R-MASS = 7.3.5
Provides: R-Matrix = 0.999375.38
Obsoletes: R-Matrix < 0.999375-7
Provides: R-methods = %{version}
Provides: R-mgcv = 1.6.1
Provides: R-nlme = 3.1.96
Provides: R-nnet = 7.3.1
Provides: R-rpart = 3.1.45
Provides: R-spatial = 7.3.1
Provides: R-rpart = 3.1.46
Provides: R-spatial = 7.3.2
Provides: R-splines = %{version}
Provides: R-stats = %{version}
Provides: R-stats4 = %{version}
Provides: R-survival = 2.35.7
Provides: R-survival = 2.35.8
Provides: R-tcltk = %{version}
Provides: R-tools = %{version}
Provides: R-utils = %{version}
Provides: R-VR = 7.3.1
%description core
A language and environment for statistical computing and graphics.
@ -108,7 +106,7 @@ Requires: R-core = %{version}-%{release}
Requires: gcc-c++, gcc-gfortran, tetex-latex
Requires: bzip2-devel, libX11-devel, pcre-devel, zlib-devel
Requires: tcl-devel, tk-devel, pkgconfig
Provides: R-Matrix-devel = 0.999375.31
Provides: R-Matrix-devel = 0.999375.38
Obsoletes: R-Matrix-devel < 0.999375-7
%description devel
@ -167,7 +165,6 @@ and header files.
%prep
%setup -q
%patch1 -p1 -b .filter-little-out
# Filter false positive provides.
cat <<EOF > %{name}-prov
@ -730,6 +727,7 @@ chmod -x $RPM_BUILD_ROOT%{_libdir}/R/library/mgcv/CITATION ${RPM_BUILD_ROOT}%{_d
%{_libdir}/R/library/survival/libs/
%{_libdir}/R/library/survival/Meta/
%{_libdir}/R/library/survival/NAMESPACE
%{_libdir}/R/library/survival/noweb/
%{_libdir}/R/library/survival/R/
# tcltk
%dir %{_libdir}/R/library/tcltk/
@ -899,6 +897,9 @@ R CMD javareconf \
%postun -n libRmath -p /sbin/ldconfig
%changelog
* Thu Apr 22 2010 Tom "spot" Callaway <tcallawa@redhat.com> - 2.11.0-1
- update to 2.11.0
* Fri Apr 02 2010 Caolán McNamara <caolanm@redhat.com> - 2.10.1-2
- rebuild for icu 4.4

2
sources
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@ -1 +1 @@
75f8b7e875b846ea96a4c6cc0abc00a4 R-2.10.1.tar.gz
c6c1e866299f533617750889c729bfb3 R-2.11.0.tar.gz