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update everyone to 2.7.2, fix security bug 460658

This commit is contained in:
Tom Callaway 2008-08-29 15:53:52 +00:00
parent 992efe1d1d
commit 900d8cad7d
3 changed files with 213 additions and 78 deletions
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27
R-2.7.1-javareconf-tmpfix.patch Normal file
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@ -0,0 +1,27 @@
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}"

262
R.spec
View File

@ -1,22 +1,25 @@
Name: R
Version: 2.5.1
Release: 2%{?dist}
Version: 2.7.2
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
# Sent upstream:
# http://bugs.r-project.org/cgi-bin/R/incoming?id=12636
Patch0: R-2.7.1-javareconf-tmpfix.patch
License: GPLv2+
Group: Applications/Engineering
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: gcc-g77
BuildRequires: gcc-c++, tetex-latex, texinfo
BuildRequires: libpng-devel, libjpeg-devel, readline-devel, libtermcap-devel
BuildRequires: XFree86-devel
BuildRequires: tcl-devel, tk-devel
BuildRequires: blas >= 3.0, pcre-devel, zlib-devel
BuildRequires: java-1.4.2-gcj-compat
BuildRequires: bzip2-devel
BuildRequires: XFree86-devel
BuildRequires: bzip2-devel, cairo-devel
Requires: ggv, cups, firefox
# These are the submodules that R provides. Sometimes R modules say they
@ -24,36 +27,32 @@ Requires: ggv, cups, firefox
# provided for packager convenience.
Provides: R-base = %{version}
Provides: R-boot = 1.2
Provides: R-class = %{version}
Provides: R-cluster = 1.11.7
Provides: R-codetools = 0.1
Provides: R-class = 7.2
Provides: R-cluster = 1.11.11
Provides: R-codetools = 0.2
Provides: R-datasets = %{version}
Provides: R-foreign = 0.8
Provides: R-graphics = %{version}
Provides: R-grDevices = %{version}
Provides: R-grid = %{version}
Provides: R-KernSmooth = 2.22
Provides: R-lattice = 0.15
Provides: R-MASS = %{version}
Provides: R-lattice = 0.17
Provides: R-MASS = 7.2
Provides: R-methods = %{version}
Provides: R-mgcv = 1.3
Provides: R-mgcv = 1.4
Provides: R-nlme = 3.1
Provides: R-nnet = %{version}
Provides: R-rcompgen = 0.1
Provides: R-nnet = 7.2
Provides: R-rpart = 3.1
Provides: R-spatial = %{version}
Provides: R-spatial = 7.2
Provides: R-splines = %{version}
Provides: R-stats = %{version}
Provides: R-stats4 = %{version}
Provides: R-survival = 2.32
Provides: R-survival = 2.34
Provides: R-tcltk = %{version}
Provides: R-tools = %{version}
Provides: R-utils = %{version}
Provides: R-VR = 7.2
# Temporary fix to avoid the SNAFU of the 0.fdr.2.* release
Conflicts: R-devel < %{version}-%{release}
%description
A language and environment for statistical computing and graphics.
R is similar to the award-winning S system, which was developed at
@ -71,12 +70,12 @@ and called at run time.
%package devel
Summary: files for development of R packages.
Group: Applications/Engineering
Requires: R = %{version}
Requires: R = %{version}-%{release}
# You need all the BuildRequires for the development version
Requires: gcc-c++, gcc-g77, tetex-latex, texinfo
Requires: libpng-devel, libjpeg-devel, readline-devel, libtermcap-devel
Requires: XFree86-devel
Requires: bzip2-devel
Requires: bzip2-devel, cairo-devel
Requires: tcl-devel, tk-devel, pkgconfig
%description devel
@ -102,6 +101,25 @@ and header files.
%prep
%setup -q
%patch0 -p1 -b .javareconf-tmpfix
# Filter false positive provides.
cat <<EOF > %{name}-prov
#!/bin/sh
%{__perl_provides} \
| grep -v 'File::Copy::Recursive' | grep -v 'Text::DelimMatch'
EOF
%define __perl_provides %{_builddir}/R-%{version}/%{name}-prov
chmod +x %{__perl_provides}
# Filter unwanted Requires:
cat << \EOF > %{name}-req
#!/bin/sh
%{__perl_requires} \
| grep -v 'perl(Text::DelimMatch)'
EOF
%define __perl_requires %{_builddir}/R-%{version}/%{name}-req
chmod +x %{__perl_requires}
%build
# Add PATHS to Renviron for R_LIBS
@ -118,11 +136,38 @@ export FPICFLAGS="-fPIC"
export FCPICFLAGS="-fPIC"
export CXXPICFLAGS="-fPIC"
%endif
case "%{_target_cpu}" in
x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
export CC="gcc -m64"
export CXX="g++ -m64"
export F77="gfortran -m64"
export FC="gfortran -m64"
;;
ia64|alpha)
export CC="gcc"
export CXX="g++"
export F77="gfortran"
export FC="gfortran"
;;
*)
export CC="gcc -m32"
export CXX="g++ -m32"
export F77="gfortran -m32"
export FC="gfortran -m32"
;;
esac
export FCFLAGS="%{optflags}"
( %configure \
--with-system-zlib --with-system-bzlib --with-system-pcre \
--with-lapack \
--with-tcl-config=%{_libdir}/tclConfig.sh \
--with-tk-config=%{_libdir}/tkConfig.sh \
--enable-R-shlib )\
--enable-R-shlib \
rdocdir=%{_docdir}/R-%{version} \
rincludedir=%{_includedir}/R \
rsharedir=%{_datadir}/R) \
| grep -A30 'R is now' - > CAPABILITIES
make
(cd src/nmath/standalone; make)
@ -131,40 +176,13 @@ make pdf
make info
%install
%makeinstall rhome=${RPM_BUILD_ROOT}%{_libdir}/R install-info
make DESTDIR=${RPM_BUILD_ROOT} install install-info install-pdf
rm -f ${RPM_BUILD_ROOT}%{_infodir}/dir
rm -f ${RPM_BUILD_ROOT}%{_infodir}/dir.old
install -p CAPABILITIES ${RPM_BUILD_ROOT}%{_docdir}/R-%{version}
#Install libRmath files
(cd src/nmath/standalone; make install \
includedir=${RPM_BUILD_ROOT}%{_includedir} \
libdir=${RPM_BUILD_ROOT}%{_libdir})
#Fix location of R_HOME_DIR in shell wrapper.
#
sed -e "s@R_HOME_DIR=.*@R_HOME_DIR=%{_libdir}/R@" < bin/R \
> ${RPM_BUILD_ROOT}%{_libdir}/R/bin/R
sed -e "s@R_HOME_DIR=.*@R_HOME_DIR=%{_libdir}/R@" < bin/R \
> ${RPM_BUILD_ROOT}%{_bindir}/R
chmod 755 ${RPM_BUILD_ROOT}%{_libdir}/R/bin/R
chmod 755 ${RPM_BUILD_ROOT}%{_bindir}/R
# Get rid of buildroot in script
for i in $RPM_BUILD_ROOT%{_libdir}/R/bin/Rscript $RPM_BUILD_ROOT%{_bindir}/Rscript $RPM_BUILD_ROOT%{_libdir}/pkgconfig/libR*.pc;
do
sed -i "s|$RPM_BUILD_ROOT||g" $i;
done
# Remove package indices. They are rebuilt by the postinstall script.
#
rm -f ${RPM_BUILD_ROOT}%{_libdir}/R/doc/html/function.html
rm -f ${RPM_BUILD_ROOT}%{_libdir}/R/doc/html/packages.html
rm -f ${RPM_BUILD_ROOT}%{_libdir}/R/doc/html/search/index.txt
# Some doc files are also installed. We don't need them
(cd %{buildroot}%{_libdir}/R;
rm -f AUTHORS COPYING COPYING.LIB COPYRIGHTS FAQ NEWS ONEWS RESOURCES THANKS)
(cd src/nmath/standalone; make install DESTDIR=${RPM_BUILD_ROOT})
mkdir -p $RPM_BUILD_ROOT/etc/ld.so.conf.d
echo "%{_libdir}/R/lib" > $RPM_BUILD_ROOT/etc/ld.so.conf.d/%{name}-%{_arch}.conf
@ -179,29 +197,45 @@ install -m0644 %{SOURCE1} $RPM_BUILD_ROOT%{_sysconfdir}/rpm/
mkdir -p $RPM_BUILD_ROOT/usr/lib/rpm/
install -m0755 %{SOURCE2} $RPM_BUILD_ROOT/usr/lib/rpm/
# Fix multilib
touch -r NEWS ${RPM_BUILD_ROOT}%{_docdir}/R-%{version}/CAPABILITIES
touch -r NEWS doc/manual/*.pdf
touch -r NEWS $RPM_BUILD_ROOT%{_bindir}/R
# Fix html/packages.html
# We can safely use RHOME here, because all of these are system packages.
sed -i 's|\..\/\..|%{_libdir}/R|g' $RPM_BUILD_ROOT%{_docdir}/R-%{version}/html/packages.html
for i in $RPM_BUILD_ROOT%{_libdir}/R/library/*/html/*.html; do
sed -i 's|\..\/\..\/..\/doc|%{_docdir}/R-%{version}|g' $i
done
%files
%defattr(-, root, root)
%{_bindir}/R
%{_bindir}/Rscript
%{_datadir}/R
%{_libdir}/R
%dir %{_libdir}/R
%{_libdir}/R/bin
%{_libdir}/R/etc
%{_libdir}/R/lib
%{_libdir}/R/library
%{_libdir}/R/modules
%{_libdir}/R/COPYING
%{_libdir}/R/NEWS
%{_libdir}/R/SVN-REVISION
/usr/lib/rpm/R-make-search-index.sh
%{_infodir}/R-*.info*
%{_sysconfdir}/rpm/macros.R
%{_mandir}/man1/*
%{_docdir}/R-%{version}
%docdir %{_docdir}/R-%{version}
/etc/ld.so.conf.d/*
%doc doc/AUTHORS CAPABILITIES doc/COPYING doc/COPYING.LIB doc/COPYRIGHTS doc/FAQ NEWS
%doc ONEWS README doc/RESOURCES doc/THANKS VERSION
%doc doc/manual/R-admin.pdf
%doc doc/manual/R-FAQ.pdf
%doc doc/manual/R-lang.pdf
%doc doc/manual/R-data.pdf
%doc doc/manual/R-intro.pdf
%files devel
%defattr(-, root, root)
%doc doc/manual/R-exts.pdf
%{_libdir}/pkgconfig/libR.pc
%{_includedir}/R
%files -n libRmath
%defattr(-, root, root)
@ -226,12 +260,18 @@ for doc in admin exts FAQ intro lang; do
fi
done
/sbin/ldconfig
R CMD javareconf > /dev/null 2>&1 || exit 0
# Update package indices
%{_bindir}/R CMD perl %{_libdir}/R/share/perl/build-help.pl --htmllists > /dev/null 2>/dev/null
%__cat %{_libdir}/R/library/*/CONTENTS > %{_libdir}/R/doc/html/search/index.txt 2>/dev/null
%__cat %{_libdir}/R/library/*/CONTENTS > %{_docdir}/R-%{version}/html/search/index.txt 2>/dev/null
# Don't use .. based paths, substitute RHOME
sed -i "s!../../..!%{_libdir}/R!g" %{_docdir}/R-%{version}/html/search/index.txt
# This could fail if there are no noarch R libraries on the system.
%__cat %{_datadir}/R/library/*/CONTENTS >> %{_libdir}/R/doc/html/search/index.txt 2>/dev/null || exit 0
%__cat %{_datadir}/R/library/*/CONTENTS >> %{_docdir}/R-%{version}/html/search/index.txt 2>/dev/null || exit 0
# Don't use .. based paths, substitute /usr/share/R
sed -i "s!../../..!/usr/share/R!g" %{_docdir}/R-%{version}/html/search/index.txt
%preun
if [ $1 = 0 ]; then
@ -242,10 +282,6 @@ if [ $1 = 0 ]; then
/sbin/install-info --delete R-${doc} %{_infodir}/dir 2>/dev/null || :
fi
done
# Remove package indices
%__rm -f %{_libdir}/R/doc/html/function.html
%__rm -f %{_libdir}/R/doc/html/packages.html
%__rm -f %{_libdir}/R/doc/html/search/index.txt
fi
%postun
@ -258,21 +294,85 @@ fi
/sbin/ldconfig
%changelog
* Fri Aug 29 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.2-1
- EL-4 VERSION
- update to 2.7.2
- fix spec for alpha compile (bz 458931)
- fix security issue in javareconf script (bz 460658)
* Mon Jul 7 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.1-1
- update to 2.7.1
* Wed May 28 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.0-5
- add cairo-devel to BR/R, so that cairo backend gets built
* Wed May 21 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.0-4
- fixup sed invocation added in -3
- make -devel package depend on base R = version-release
- fix bad paths in package html files
* Wed May 21 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.0-3
- fix poorly constructed file paths in html/packages.html (bz 442727)
* Tue May 13 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.0-2
- add patch from Martyn Plummer to avoid possible bad path hardcoding in
/usr/bin/Rscript
- properly handle ia64 case (bz 446181)
* Mon Apr 28 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.7.0-1
- update to 2.70
- rcompgen is no longer a standalone package
- redirect javareconf to /dev/null (bz 442366)
* Fri Feb 8 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.2-1
- properly version the items in the VR bundle
- 2.6.2
- don't use setarch for java setup
- fix R post script file
* Thu Jan 31 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.1-4
- multilib handling (thanks Martyn Plummer)
- Update indices in the right place.
* Mon Jan 7 2008 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.1-3
- move INSTALL back into R main package, as it is useful without the
other -devel bits (e.g. installing noarch package from CRAN)
* Tue Dec 11 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.1-2
- based on changes from Martyn Plummer <martyn.plummer@r-project.org>
- use configure options rdocdir, rincludedir, rsharedir
- use DESTDIR at installation
- remove obsolete generation of packages.html
- move header files and INSTALL R-devel package
* Mon Nov 26 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.1-1
- bump to 2.6.1
* Tue Oct 30 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.0-3.1
- fix missing perl requires
* Mon Oct 29 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.0-3
- fix multilib conflicts (bz 343061)
* Mon Oct 29 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.0-2
- add R CMD javareconf to post (bz 354541)
- don't pickup bogus perl provides (bz 356071)
- use xdg-open, drop requires for firefox/evince (bz 351841)
* Thu Oct 4 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.6.0-1
- bump to 2.6.0
* Sun Aug 26 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.1-3
- fix license tag
- rebuild for ppc32
* Thu Jul 5 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.1-2
- add rpm helper macros, script
* Tue Jul 3 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.1-1.1
- fix ppc on EL-4
* Mon Jul 2 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.1-1
- drop patch, upstream fixed
- bump to 2.5.1
* Fri May 25 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.0-3
- add missing BR: bzip2-devel, libXmu-devel
- cleanup macros from changelog
- switch from termcap to ncurses
* Mon Apr 30 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.5.0-2
- patch from Martyn Plummer fixes .pc files
- add new BR: gcc-objc
@ -281,8 +381,16 @@ fi
- bump to 2.5.0
* Tue Mar 13 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.4.1-4
- get rid of termcap related requires, replace with ncurses
- use java-1.5.0-gcj instead of old java-1.4.2
- add /usr/share/R/library as a valid R_LIBS directory for noarch bits
* Sun Feb 25 2007 Jef Spaleta <jspaleta@gmail.com> 2.4.1-3
- rebuild for reverted tcl/tk
* Fri Feb 2 2007 Tom "spot" Callaway <tcallawa@redhat.com> 2.4.1-2
- rebuild for new tcl/tk
* Tue Dec 19 2006 Tom "spot" Callaway <tcallawa@redhat.com> 2.4.1-1
- bump to 2.4.1
- fix install-info invocations in post/preun (bz 219407)
@ -441,8 +549,8 @@ fi
avoiding warnings about UTF-8 locale not being supported
* Mon Mar 15 2004 Martyn Plummer <plummer@iarc.fr>
- No need to export optimization flags. This is done by %%configure
- Folded info installation into %%makeinstall
- No need to export optimization flags. This is done by %configure
- Folded info installation into %makeinstall
- Check that RPM_BASE_ROOT is not set to "/" before cleaning up
* Thu Feb 03 2004 Martyn Plummer <plummer@iarc.fr>
@ -451,7 +559,7 @@ fi
* Tue Feb 03 2004 Martyn Plummer <plummer@iarc.fr>
- Changes from James Henstridge <james@daa.com.au> to allow building on IA64:
- Added BuildRequires for tcl-devel tk-devel tetex-latex
- Use the %%configure macro to call the configure script
- Use the %configure macro to call the configure script
- Pass --with-tcl-config and --with-tk-config arguments to configure
- Set rhome to point to the build root during "make install"

2
sources
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@ -1 +1 @@
162f6d5a1bd7c60fd652145e050f3f3c R-2.5.1.tar.gz
6122945e9301825b97a506151b3cefde R-2.7.2.tar.gz