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Merge branch 'master' into el5

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This commit is contained in:
Tom Callaway 2016-05-10 12:17:53 -04:00
commit 0d37da678c
5 changed files with 61 additions and 31 deletions

2
.gitignore vendored

@ -1,2 +1,4 @@
/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

14
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

12
R-3.3.0-fix-java_path-in-javareconf.patch Normal file

@ -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

62
R.spec

@ -55,8 +55,8 @@
%global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d)
Name: R
Version: 3.2.3
Release: 4%{?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}.tar.gz
@ -77,7 +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
Patch1: 0001-Wait-for-MapNotify-event-while-intializing-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)
@ -112,6 +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
@ -124,6 +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
@ -181,9 +185,9 @@ Requires: perl, sed, gawk, tex(latex), less, make, unzip
# depend on one of these submodules rather than just R. These are provided for
# packager convenience.
Provides: R-base = %{version}
Provides: R-boot = 1.3.17
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
@ -193,19 +197,19 @@ 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 = 1.2.3
Provides: R-Matrix = 1.2.6
Obsoletes: R-Matrix < 0.999375-7
Provides: R-methods = %{version}
Provides: R-mgcv = 1.8.9
Provides: R-nlme = 3.1.122
Provides: R-nnet = 7.3.11
Provides: R-mgcv = 1.8.12
Provides: R-nlme = 3.1.127
Provides: R-nnet = 7.3.12
Provides: R-parallel = %{version}
Provides: R-rpart = 4.1.10
Provides: R-spatial = 7.3.10
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}
@ -257,7 +261,7 @@ Requires: tex(cm-super-ts1.enc)
Requires: qpdf
%endif
Provides: R-Matrix-devel = 1.2.3
Provides: R-Matrix-devel = 1.2.6
Obsoletes: R-Matrix-devel < 0.999375-7
%if %{modern}
@ -289,9 +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
@ -349,9 +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
%setup -q -n %{name}-%{version}
%patch0 -p1 -b .disable-backing-store
%patch1 -p1 -b .wait-for-map-notify
%patch1 -p1 -b .fixpath
# Filter false positive provides.
cat <<EOF > %{name}-prov
@ -359,6 +363,7 @@ cat <<EOF > %{name}-prov
%{__perl_provides} \
| grep -v 'File::Copy::Recursive' | grep -v 'Text::DelimMatch'
EOF
%global __perl_provides %{_builddir}/R-%{version}/%{name}-prov
chmod +x %{__perl_provides}
@ -427,19 +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 \
@ -754,6 +758,7 @@ make check
%{_libdir}/R/library/Matrix/include/
%{_libdir}/R/library/Matrix/INDEX
%{_libdir}/R/library/Matrix/libs/
%{_libdir}/R/library/Matrix/LICENCE
%{_libdir}/R/library/Matrix/Meta/
%{_libdir}/R/library/Matrix/NAMESPACE
%{_libdir}/R/library/Matrix/NEWS.Rd
@ -991,6 +996,21 @@ 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
* Fri Mar 18 2016 Tom Callaway <spot@fedoraproject.org> - 3.2.4-1
- move to 3.2.4-revised
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 3.2.3-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Tue Jan 26 2016 Tom Callaway <spot@fedoraproject.org> - 3.2.3-4
- if texi2any is set to 0, then copy in prebuilt html manuals (RHEL 5 & 6 only)

2
sources

@ -1 +1 @@
1ba3dac113efab69e706902810cc2970 R-3.2.3.tar.gz
5a7506c8813432d1621c9725e86baf7a R-3.3.0.tar.gz