From 9aa74510086346439cebb90b1cb5ac590a8a1b97 Mon Sep 17 00:00:00 2001 From: Tom Callaway Date: Tue, 10 May 2016 11:49:28 -0400 Subject: [PATCH] 3.3.0 --- .gitignore | 1 + ...-Disable-backing-store-in-X11-window.patch | 14 ++---- R-3.3.0-fix-java_path-in-javareconf.patch | 12 +++++ R.spec | 49 +++++++++++-------- sources | 2 +- 5 files changed, 48 insertions(+), 30 deletions(-) create mode 100644 R-3.3.0-fix-java_path-in-javareconf.patch diff --git a/.gitignore b/.gitignore index 643d4cf..b3f6bd0 100644 --- a/.gitignore +++ b/.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 diff --git a/0001-Disable-backing-store-in-X11-window.patch b/0001-Disable-backing-store-in-X11-window.patch index 7989daf..21fe517 100644 --- a/0001-Disable-backing-store-in-X11-window.patch +++ b/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 - diff --git a/R-3.3.0-fix-java_path-in-javareconf.patch b/R-3.3.0-fix-java_path-in-javareconf.patch new file mode 100644 index 0000000..6453f92 --- /dev/null +++ b/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 diff --git a/R.spec b/R.spec index 98ab107..a9a6540 100644 --- a/R.spec +++ b/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 < %{name}-prov @@ -358,8 +364,7 @@ cat < %{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 - 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 - 3.2.4-2 - rebuild for ICU 57.1 diff --git a/sources b/sources index f776cd5..2f8e0c1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -552b0c8088bab08ca4188797b919a58f R-3.2.4-revised.tar.gz +5a7506c8813432d1621c9725e86baf7a R-3.3.0.tar.gz