3.3.0

.gitignore

@@ -22,3 +22,4 @@ R-2.11.1.tar.gz
 /R-3.2.2.tar.gz
 /R-3.2.3.tar.gz
 /R-3.2.4-revised.tar.gz
+/R-3.3.0.tar.gz

0001-Disable-backing-store-in-X11-window.patch

@@ -8,19 +8,15 @@ Xorg server will not generate Expose events if backing store is enabled. Since i
  src/modules/X11/devX11.c |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
-diff --git a/src/modules/X11/devX11.c b/src/modules/X11/devX11.c
-index b714f1a..143441f 100644
---- a/src/modules/X11/devX11.c
-+++ b/src/modules/X11/devX11.c
-@@ -1477,7 +1477,7 @@ X11_Open(pDevDesc dd, pX11Desc xd, const char *dsp,
+diff -up R-3.3.0/src/modules/X11/devX11.c.disable-backing-store R-3.3.0/src/modules/X11/devX11.c
+--- R-3.3.0/src/modules/X11/devX11.c.disable-backing-store	2016-05-10 09:54:12.440997353 -0400
++++ R-3.3.0/src/modules/X11/devX11.c	2016-05-10 09:54:48.560701316 -0400
+@@ -1479,7 +1479,7 @@ X11_Open(pDevDesc dd, pX11Desc xd, const
      memset(&attributes, 0, sizeof(attributes));
      attributes.background_pixel = whitepixel;
      attributes.border_pixel = blackpixel;
 -    attributes.backing_store = Always;
 +    attributes.backing_store = NotUseful;
      attributes.event_mask = ButtonPressMask 
-       | ButtonMotionMask 
+       | PointerMotionMask 
        | PointerMotionHintMask
--- 
-1.7.1
-

R-3.3.0-fix-java_path-in-javareconf.patch

@@ -0,0 +1,12 @@
+diff -up R-3.3.0/src/scripts/javareconf.in.fixpath R-3.3.0/src/scripts/javareconf.in
+--- R-3.3.0/src/scripts/javareconf.in.fixpath	2016-05-10 11:13:49.539844250 -0400
++++ R-3.3.0/src/scripts/javareconf.in	2016-05-10 11:15:10.475180907 -0400
+@@ -78,7 +78,7 @@ else
+ 	JAVA_PATH=${PATH}
+     else
+ 	## try jre/bin first just in case we don't have full JDK
+-	JAVA_PATH=${JAVA_HOME}:${JAVA_HOME}/jre/bin:${JAVA_HOME}/bin:${JAVA_HOME}/../bin:${PATH}
++	JAVA_PATH=${JAVA_HOME}:${JAVA_HOME}/jre/bin:${PATH}:${JAVA_HOME}/bin:${JAVA_HOME}/../bin
+     fi
+ fi
+ ## if 'java' is not on the PATH or JAVA_HOME, add some guesses as of

R.spec

@@ -55,11 +55,11 @@
 %global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d)
 
 Name: R
-Version: 3.2.4
-Release: 2%{?dist}
+Version: 3.3.0
+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-3/R-%{version}-revised.tar.gz
+Source0: ftp://cran.r-project.org/pub/R/src/base/R-3/R-%{version}.tar.gz
 Source1: macros.R
 Source2: R-make-search-index.sh
 %if %{texi2any}
@@ -77,6 +77,8 @@ Source105: https://cran.r-project.org/doc/manuals/r-release/R-ints.html
 Source106: https://cran.r-project.org/doc/FAQ/R-FAQ.html
 %endif
 Patch0: 0001-Disable-backing-store-in-X11-window.patch
+# see https://bugzilla.redhat.com/show_bug.cgi?id=1324145
+Patch1: R-3.3.0-fix-java_path-in-javareconf.patch
 License: GPLv2+
 Group: Applications/Engineering
 BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
@@ -111,6 +113,8 @@ BuildRequires: tre-devel
 BuildRequires: autoconf, automake, libtool
 %endif
 
+# We use the bundled lapack and shim for BLAS now.
+%if 0
 %if 0%{?fedora} >= 21
 BuildRequires: lapack-devel >= 3.5.0-7
 BuildRequires: blas-devel >= 3.5.0-7
@@ -123,6 +127,7 @@ BuildRequires: lapack-devel
 BuildRequires: blas-devel >= 3.0
 %endif
 %endif
+%endif
 
 BuildRequires: libSM-devel, libX11-devel, libICE-devel, libXt-devel
 BuildRequires: bzip2-devel, libXmu-devel, cairo-devel, libtiff-devel
@@ -182,7 +187,7 @@ Requires: perl, sed, gawk, tex(latex), less, make, unzip
 Provides: R-base = %{version}
 Provides: R-boot = 1.3.18
 Provides: R-class = 7.3.14
-Provides: R-cluster = 2.0.3
+Provides: R-cluster = 2.0.4
 Provides: R-codetools = 0.2.14
 Provides: R-datasets = %{version}
 Provides: R-foreign = 0.8.66
@@ -192,11 +197,11 @@ Provides: R-grid = %{version}
 Provides: R-KernSmooth = 2.23.15
 Provides: R-lattice = 0.20.33
 Provides: R-MASS = 7.3.45
-Provides: R-Matrix = 1.2.4
+Provides: R-Matrix = 1.2.6
 Obsoletes: R-Matrix < 0.999375-7
 Provides: R-methods = %{version}
 Provides: R-mgcv = 1.8.12
-Provides: R-nlme = 3.1.125
+Provides: R-nlme = 3.1.127
 Provides: R-nnet = 7.3.12
 Provides: R-parallel = %{version}
 Provides: R-rpart = 4.1.10
@@ -204,7 +209,7 @@ Provides: R-spatial = 7.3.11
 Provides: R-splines = %{version}
 Provides: R-stats = %{version}
 Provides: R-stats4 = %{version}
-Provides: R-survival = 2.38.3
+Provides: R-survival = 2.39.2
 Provides: R-tcltk = %{version}
 Provides: R-tools = %{version}
 Provides: R-utils = %{version}
@@ -256,7 +261,7 @@ Requires: tex(cm-super-ts1.enc)
 Requires: qpdf
 %endif
 
-Provides: R-Matrix-devel = 1.2.4
+Provides: R-Matrix-devel = 1.2.6
 Obsoletes: R-Matrix-devel < 0.999375-7
 
 %if %{modern}
@@ -288,9 +293,9 @@ Summary: R with Fedora provided Java Runtime Environment
 Group: Applications/Engineering
 Requires(post): R-core = %{version}-%{release}
 %if %{with_java_headless}
-Requires(post): java-headless
+Requires: java-headless
 %else
-Requires(post): java
+Requires: java
 %endif
 
 %description java
@@ -348,8 +353,9 @@ A standalone library of mathematical and statistical functions derived
 from the R project.  This package provides the static libRmath library.
 
 %prep
-%setup -q -n %{name}-revised
+%setup -q -n %{name}-%{version}
 %patch0 -p1 -b .disable-backing-store
+%patch1 -p1 -b .fixpath
 
 # Filter false positive provides.
 cat <<EOF > %{name}-prov
@@ -358,8 +364,7 @@ cat <<EOF > %{name}-prov
 | grep -v 'File::Copy::Recursive' | grep -v 'Text::DelimMatch'
 EOF
 
-# %%global __perl_provides %%{_builddir}/R-%%{version}/%%{name}-prov
-%global __perl_provides %{_builddir}/R-revised/%{name}-prov
+%global __perl_provides %{_builddir}/R-%{version}/%{name}-prov
 chmod +x %{__perl_provides}
 
 # Filter unwanted Requires:
@@ -368,8 +373,7 @@ cat << \EOF > %{name}-req
 %{__perl_requires} \
 | grep -v 'perl(Text::DelimMatch)'
 EOF
-# %%global __perl_requires %%{_builddir}/R-%%{version}/%%{name}-req
-%global __perl_requires %{_builddir}/R-revised/%{name}-req
+%global __perl_requires %{_builddir}/R-%{version}/%{name}-req
 chmod +x %{__perl_requires}
 
 %build
@@ -428,19 +432,18 @@ export FCFLAGS="%{optflags}"
 # https://bugzilla.redhat.com/show_bug.cgi?id=1117496
 # https://bugzilla.redhat.com/show_bug.cgi?id=1117497
 #
-# Also, --enable-BLAS-shlib would be nice to enable
-# as a shim to the system blas but it unfortunately 
-# enables the bundled Rlapack (not a shim to the system lapack).
+# We use --enable-BLAS-shlib here. It generates a shared library
+# of the R bundled blas, that can be replaced by an optimized version.
+# It also results in R using the bundled lapack copy.
 
 ( %configure \
 %if %{system_tre}
     --with-system-tre \
 %endif
-    --with-system-zlib --with-system-bzlib --with-system-pcre \
     --with-system-valgrind-headers \
 %if 0%{?fedora}
     --with-lapack \
-    --with-blas \
+    --enable-BLAS-shlib \
 %endif
     --with-tcl-config=%{_libdir}/tclConfig.sh \
     --with-tk-config=%{_libdir}/tkConfig.sh \
@@ -993,6 +996,12 @@ R CMD javareconf \
 %postun -n libRmath -p /sbin/ldconfig
 
 %changelog
+* Tue May 10 2016 Tom Callaway <spot@fedoraproject.org> - 3.3.0-1
+- update to 3.3.0
+- fix R-java Requires (bz1324145)
+- fix JAVA_PATH definition in javareconf (bz1324145)
+- use bundled BLAS and LAPACK, create shared library for Rblas
+
 * Fri Apr 15 2016 David Tardon <dtardon@redhat.com> - 3.2.4-2
 - rebuild for ICU 57.1
 

sources

@@ -1 +1 @@
-552b0c8088bab08ca4188797b919a58f  R-3.2.4-revised.tar.gz
+5a7506c8813432d1621c9725e86baf7a  R-3.3.0.tar.gz