4.0.3

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.gitignore

@@ -34,3 +34,10 @@
 /pcre-8.43.tar.bz2
 /curl-7.67.0.tar.bz2
 /R-3.6.3.tar.gz
+/R-4.0.0.tar.gz
+/R-4.0.1.tar.gz
+/R-4.0.2.tar.gz
+/xz-5.2.5.tar.bz2
+/R-4.0.3.tar.gz
+/pcre-8.44.tar.bz2
+/curl-7.72.0.tar.bz2

R-4.0.0-ppc64-infinite-loop-fix.patch

@@ -0,0 +1,50 @@
+diff -up R-4.0.0/src/main/machar.c.ppc64 R-4.0.0/src/main/machar.c
+--- R-4.0.0/src/main/machar.c.ppc64	2020-06-02 14:42:18.741222048 -0400
++++ R-4.0.0/src/main/machar.c	2020-06-02 14:44:26.523106368 -0400
+@@ -98,21 +98,22 @@ MACH_NAME(int *ibeta, int *it, int *irnd
+ {
+ 	volatile DTYPE a, b, beta, betain, betah, one,
+ 		t, temp, tempa, temp1, two, y, z, zero;
+-	int i, itemp, iz, j, k, mx, nxres;
++	int i, iz, j, k, mx, nxres;
+ 
+ 	one = 1;
+ 	two = one+one;
+ 	zero = one-one;
+ 
+ 		/* determine ibeta, beta ala malcolm. */
+-
+-	a = one;
++	a = one; // a = <large> = 9.0072e+15 for 'double' is used later
+ 	do {
+ 		a = a + a;
+ 		temp = a + one;
+ 		temp1 = temp - a;
+ 	}
+ 	while(temp1 - one == zero);
++#ifdef _no_longer___did_overflow_ // on IBM PowerPPC ('Power 8')
++	int itemp;
+ 	b = one;
+ 	do {
+ 		b = b + b;
+@@ -121,6 +122,9 @@ MACH_NAME(int *ibeta, int *it, int *irnd
+ 	}
+ 	while (itemp == 0);
+ 	*ibeta = itemp;
++#else
++	*ibeta = (int) FLT_RADIX;
++#endif
+ 	beta = *ibeta;
+ 
+ 		/* determine it, irnd */
+diff -up R-4.0.0/src/main/platform.c.ppc64 R-4.0.0/src/main/platform.c
+--- R-4.0.0/src/main/platform.c.ppc64	2020-06-02 14:44:40.940754817 -0400
++++ R-4.0.0/src/main/platform.c	2020-06-02 14:45:08.940072121 -0400
+@@ -43,6 +43,7 @@
+ #include <Rinterface.h>
+ #include <Fileio.h>
+ #include <ctype.h>			/* toupper */
++#include <float.h> // -> FLT_RADIX
+ #include <limits.h>
+ #include <string.h>
+ #include <stdlib.h>			/* for realpath */

R.spec

@@ -4,10 +4,11 @@
 %global runjavareconf 1
 
 # lapack comes from openblas, whenever possible.
-# We decided to implement this change in Fedora 32+ and EPEL-8 only.
+# We decided to implement this change in Fedora 31+ and EPEL-8 only.
 # This was to minimize the impact on end-users who might have R modules
 # installed locally with the old dependency on libRlapack.so
-%if 0%{?fedora} >= 32
+
+%if 0%{?fedora} >= 31
 %global syslapack 1
 %else
 %if 0%{?rhel} && 0%{?rhel} >= 8
@@ -35,6 +36,12 @@
  %endif
 %endif
 
+%if 0%{?fedora} >= 33
+%global flexiblas 1
+%else
+%global flexiblas 0
+%endif
+
 %if 0%{?fedora} >= 31
 %global usemacros 1
 %else
@@ -146,12 +153,16 @@
 %global texi2any 1
 %endif
 
+%global major_version 4
+%global minor_version 0
+%global patch_version 3
+
 Name: R
-Version: 3.6.3
+Version: %{major_version}.%{minor_version}.%{patch_version}
 Release: 1%{?dist}
 Summary: A language for data analysis and graphics
 URL: http://www.r-project.org
-Source0: https://cran.r-project.org/src/base/R-3/R-%{version}.tar.gz
+Source0: https://cran.r-project.org/src/base/R-4/R-%{version}.tar.gz
 %if %{texi2any}
 # If we have texi2any 5.1+, we can generate the docs on the fly.
 # If not, we're building for a very old target (RHEL 6 or older)
@@ -169,9 +180,9 @@ Source106: https://cran.r-project.org/doc/FAQ/R-FAQ.html
 %if %{zlibhack}
 %global zlibv 1.2.11
 %global bzipv 1.0.8
-%global xzv 5.2.4
-%global pcrev 8.43
-%global curlv 7.67.0
+%global xzv 5.2.5
+%global pcrev 8.44
+%global curlv 7.72.0
 Source1000: http://zlib.net/zlib-%{zlibv}.tar.gz
 Source1001: https://www.sourceware.org/pub/bzip2/bzip2-%{bzipv}.tar.gz
 Source1002: http://tukaani.org/xz/xz-%{xzv}.tar.bz2
@@ -232,16 +243,22 @@ BuildRequires: java
 BuildRequires: tre-devel
 BuildRequires: autoconf, automake, libtool
 %endif
+%if %{flexiblas}
+BuildRequires: flexiblas-devel
+%else
 %if %{openblas}
 BuildRequires: openblas-devel
 %endif
+%endif
 
 %if %{syslapack}
+%if !%{flexiblas}
 %if !%{openblas}
 BuildRequires: lapack-devel >= 3.5.0-7
 BuildRequires: blas-devel >= 3.5.0-7
 %endif
 %endif
+%endif
 
 BuildRequires: libSM-devel, libX11-devel, libICE-devel, libXt-devel
 BuildRequires: bzip2-devel, libXmu-devel, cairo-devel, libtiff-devel
@@ -286,7 +303,9 @@ and called at run time.
 
 %package core
 Summary: The minimal R components necessary for a functional runtime
-Requires: xdg-utils, cups
+Requires: xdg-utils
+# Bugzilla 1875165
+Recommends: cups
 # R inherits the compiler flags it was built with, hence we need this on hardened systems
 %if 0%{hardening}
 Requires: redhat-rpm-config
@@ -306,16 +325,22 @@ Requires: sed, gawk, tex(latex), less, make, unzip
 Requires: libRmath%{?_isa} = %{version}-%{release}
 
 %if !%{syslapack}
+%if !%{flexiblas}
 %if %{openblas}
 Requires: openblas-Rblas
 %endif
 %endif
+%endif
 
 %if %{use_devtoolset}
 # We need it for CXX11 and higher support.
 Requires: devtoolset-%{dts_version}-toolchain
 %endif
 
+# This is our ABI provides to prevent mismatched installs.
+# R packages should autogenerate a Requires: R(ABI) based on the R they were built against.
+Provides: R(ABI) = %{major_version}.%{minor_version}
+
 # These are the submodules that R-core provides. Sometimes R modules say they
 # depend on one of these submodules rather than just R. These are provided for
 # packager convenience.
@@ -327,32 +352,32 @@ Requires: devtoolset-%{dts_version}-toolchain
   print("Provides: R(" .. name .. ") = " .. version)
 }
 %add_submodule base %{version}
-%add_submodule boot 1.3-24
-%add_submodule class 7.3-15
+%add_submodule boot 1.3-25
+%add_submodule class 7.3-17
 %add_submodule cluster 2.1.0
 %add_submodule codetools 0.2-16
 %add_submodule compiler %{version}
 %add_submodule datasets %{version}
-%add_submodule foreign 0.8-75
+%add_submodule foreign 0.8-80
 %add_submodule graphics %{version}
 %add_submodule grDevices %{version}
 %add_submodule grid %{version}
-%add_submodule KernSmooth 2.23-16
-%add_submodule lattice 0.20-38
-%add_submodule MASS 7.3-51.5
+%add_submodule KernSmooth 2.23-17
+%add_submodule lattice 0.20-41
+%add_submodule MASS 7.3-53
 %add_submodule Matrix 1.2-18
 Obsoletes: R-Matrix < 0.999375-7
 %add_submodule methods %{version}
-%add_submodule mgcv 1.8-31
-%add_submodule nlme 3.1-144
-%add_submodule nnet 7.3-12
+%add_submodule mgcv 1.8-33
+%add_submodule nlme 3.1-149
+%add_submodule nnet 7.3-14
 %add_submodule parallel %{version}
 %add_submodule rpart 4.1-15
-%add_submodule spatial 7.3-11
+%add_submodule spatial 7.3-12
 %add_submodule splines %{version}
 %add_submodule stats %{version}
 %add_submodule stats4 %{version}
-%add_submodule survival 3.1-8
+%add_submodule survival 3.2-7
 %add_submodule tcltk %{version}
 %add_submodule tools %{version}
 %add_submodule translations %{version}
@@ -386,10 +411,14 @@ Requires: pcre-devel
 Requires: pcre2-devel
 %endif
 %if %{syslapack}
+%if %{flexiblas}
+Requires: flexiblas-devel
+%else
 %if %{openblas}
 Requires: openblas-devel
 %endif
 %endif
+%endif
 %if %{modern}
 Requires: libicu-devel
 %endif
@@ -644,6 +673,11 @@ export FFLAGS="%{optflags} --no-optimize-sibling-calls"
 # of the R bundled blas, that can be replaced by an optimized version.
 # It also results in R using the bundled lapack copy.
 
+%if %{flexiblas}
+# avoid this check
+sed -i '/"checking whether the BLAS is complete/i r_cv_complete_blas=yes' configure
+%endif
+
 ( %configure \
 %if 0%{?rhel} && 0%{?rhel} <= 5
     --with-readline=no \
@@ -654,7 +688,11 @@ export FFLAGS="%{optflags} --no-optimize-sibling-calls"
     --with-system-valgrind-headers \
 %if %{syslapack}
     --with-lapack \
+%if %{flexiblas}
+    --with-blas="flexiblas" \
+%else
     --with-blas \
+%endif
 %else
     --enable-BLAS-shlib \
 %endif
@@ -676,8 +714,7 @@ export FFLAGS="%{optflags} --no-optimize-sibling-calls"
 %endif
     rdocdir=%{?_pkgdocdir}%{!?_pkgdocdir:%{_docdir}/%{name}-%{version}} \
     rincludedir=%{_includedir}/R \
-    rsharedir=%{_datadir}/R) \
- > CONFIGURE.log
+    rsharedir=%{_datadir}/R) | tee CONFIGURE.log
 cat CONFIGURE.log | grep -A30 'R is now' - > CAPABILITIES
 %if 0%{?zlibhack}
 make V=1 CURL_CPPFLAGS='-DCURL_STATICLIB -I%{_builddir}/%{name}-%{version}/curl-%{curlv}/target%{_includedir}' CURL_LIBS=`%{_builddir}/%{name}-%{version}/curl-%{curlv}/target/usr/bin/curl-config --libs`
@@ -800,11 +837,13 @@ sed -i 's|/builddir/build/BUILD/R-%{version}/curl-%{curlv}/target%{_libdir}/:/bu
 %endif
 
 %if !%{syslapack}
+%if !%{flexiblas}
 %if %{openblas}
 # Rename the R blas so.
 mv %{buildroot}%{_libdir}/R/lib/libRblas.so %{buildroot}%{_libdir}/R/lib/libRrefblas.so
 %endif
 %endif
+%endif
 
 # okay, look. its very clear that upstream does not run the test suite on any non-intel architectures.
 %check
@@ -825,9 +864,9 @@ R CMD javareconf \
     JAVA_HOME=%{_jvmdir}/jre \
     JAVA_CPPFLAGS='-I%{_jvmdir}/java/include\ -I%{_jvmdir}/java/include/linux' \
     JAVA_LIBS='-L%{_jvmdir}/jre/lib/%{java_arch}/server \
-    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch} \
+    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch}\ -L%{_jvmdir}/jre/lib/server \
     -L/usr/java/packages/lib/%{java_arch}\ -L/lib\ -L/usr/lib\ -ljvm' \
-    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
+    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
     > /dev/null 2>&1 || exit 0
 %endif
 
@@ -859,9 +898,9 @@ R CMD javareconf \
     JAVA_HOME=%{_jvmdir}/jre \
     JAVA_CPPFLAGS='-I%{_jvmdir}/java/include\ -I%{_jvmdir}/java/include/linux' \
     JAVA_LIBS='-L%{_jvmdir}/jre/lib/%{java_arch}/server \
-    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch} \
+    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch}\ -L%{_jvmdir}/jre/lib/server \
     -L/usr/java/packages/lib/%{java_arch}\ -L/lib\ -L/usr/lib\ -ljvm' \
-    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
+    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
     > /dev/null 2>&1 || exit 0
 %endif
 
@@ -871,9 +910,9 @@ R CMD javareconf \
     JAVA_HOME=%{_jvmdir}/jre \
     JAVA_CPPFLAGS='-I%{_jvmdir}/java/include\ -I%{_jvmdir}/java/include/linux' \
     JAVA_LIBS='-L%{_jvmdir}/jre/lib/%{java_arch}/server \
-    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch} \
+    -L%{_jvmdir}/jre/lib/%{java_arch}\ -L%{_jvmdir}/java/lib/%{java_arch}\ -L%{_jvmdir}/jre/lib/server \
     -L/usr/java/packages/lib/%{java_arch}\ -L/lib\ -L/usr/lib\ -ljvm' \
-    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
+    JAVA_LD_LIBRARY_PATH=%{_jvmdir}/jre/lib/%{java_arch}/server:%{_jvmdir}/jre/lib/%{java_arch}:%{_jvmdir}/java/lib/%{java_arch}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
     > /dev/null 2>&1 || exit 0
 %endif
 %endif
@@ -933,6 +972,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/boot/po/de/
 %lang(en) %{_libdir}/R/library/boot/po/en*/
 %lang(fr) %{_libdir}/R/library/boot/po/fr/
+%lang(it) %{_libdir}/R/library/boot/po/it/
 %lang(ko) %{_libdir}/R/library/boot/po/ko/
 %lang(pl) %{_libdir}/R/library/boot/po/pl/
 %lang(ru) %{_libdir}/R/library/boot/po/ru/
@@ -952,6 +992,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/class/po/de/
 %lang(en) %{_libdir}/R/library/class/po/en*/
 %lang(fr) %{_libdir}/R/library/class/po/fr/
+%lang(it) %{_libdir}/R/library/class/po/it/
 %lang(ko) %{_libdir}/R/library/class/po/ko/
 %lang(pl) %{_libdir}/R/library/class/po/pl/
 %{_libdir}/R/library/class/R/
@@ -1003,6 +1044,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/foreign/po/de/
 %lang(en) %{_libdir}/R/library/foreign/po/en*/
 %lang(fr) %{_libdir}/R/library/foreign/po/fr/
+%lang(it) %{_libdir}/R/library/foreign/po/it/
 %lang(pl) %{_libdir}/R/library/foreign/po/pl/
 %{_libdir}/R/library/foreign/R/
 # graphics
@@ -1024,6 +1066,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/KernSmooth/po/de/
 %lang(en) %{_libdir}/R/library/KernSmooth/po/en*/
 %lang(fr) %{_libdir}/R/library/KernSmooth/po/fr/
+%lang(it) %{_libdir}/R/library/KernSmooth/po/it/
 %lang(ko) %{_libdir}/R/library/KernSmooth/po/ko/
 %lang(pl) %{_libdir}/R/library/KernSmooth/po/pl/
 %{_libdir}/R/library/KernSmooth/R/
@@ -1063,6 +1106,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/MASS/po/de/
 %lang(en) %{_libdir}/R/library/MASS/po/en*/
 %lang(fr) %{_libdir}/R/library/MASS/po/fr/
+%lang(it) %{_libdir}/R/library/MASS/po/it/
 %lang(ko) %{_libdir}/R/library/MASS/po/ko/
 %lang(pl) %{_libdir}/R/library/MASS/po/pl/
 %{_libdir}/R/library/MASS/R/
@@ -1134,6 +1178,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/nnet/po/de/
 %lang(en) %{_libdir}/R/library/nnet/po/en*/
 %lang(fr) %{_libdir}/R/library/nnet/po/fr/
+%lang(it) %{_libdir}/R/library/nnet/po/it/
 %lang(ko) %{_libdir}/R/library/nnet/po/ko/
 %lang(pl) %{_libdir}/R/library/nnet/po/pl/
 %{_libdir}/R/library/nnet/R/
@@ -1174,6 +1219,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/spatial/po/de/
 %lang(en) %{_libdir}/R/library/spatial/po/en*/
 %lang(fr) %{_libdir}/R/library/spatial/po/fr/
+%lang(it) %{_libdir}/R/library/spatial/po/it/
 %lang(ko) %{_libdir}/R/library/spatial/po/ko/
 %lang(pl) %{_libdir}/R/library/spatial/po/pl/
 %{_libdir}/R/library/spatial/ppdata/
@@ -1234,6 +1280,39 @@ R CMD javareconf \
 %{_libdir}/libRmath.a
 
 %changelog
+* Mon Oct 12 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.3-1
+- update to 4.0.3
+
+* Tue Sep  8 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.2-5
+- make cups a "Recommends" instead of a "Requires" (bz1875165)
+- even though f31 uses a forked spec file, reflect the systemlapack change there here
+
+* Fri Aug 07 2020 Iñaki Úcar <iucar@fedoraproject.org> - 4.0.2-4
+- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
+
+* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 4.0.2-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Wed Jul 15 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.2-2
+- add additional paths to find libjvm.so (OpenJDK 11+)
+
+* Mon Jun 22 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.2-1
+- update to 4.0.2
+
+* Tue Jun 16 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.1-1
+- update to 4.0.1
+
+* Mon Jun 15 2020 Pete Walter <pwalter@fedoraproject.org> - 4.0.0-3
+- Rebuild for ICU 67
+
+* Tue Jun 2 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.0-2
+- apply upstream fix for ppc64 infinite loop
+
+* Fri May 8 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.0-1
+- update to 4.0.0
+  NOTE: This major release update requires all installed R modules to be rebuilt in order to work.
+  To help with this, we've added an R(ABI) Provides/Requires setup.
+
 * Mon Mar  2 2020 Tom Callaway <spot@fedoraproject.org> - 3.6.3-1
 - update to 3.6.3
 - conditionalize lapack changes from previous commits to Fedora 32+ and EPEL-8

sources

@@ -1,6 +1,6 @@
 SHA512 (zlib-1.2.11.tar.gz) = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
-SHA512 (xz-5.2.4.tar.bz2) = 25a548c34a304ba51cdaa63813df0fa4ac2f3cf0ec6dc2d181ec5b62fe586090cd0f1c866ee7ba19e9b264ecabf9ca9f2f1dda7f95313546da4152f3cfaa7e6e
 SHA512 (bzip2-1.0.8.tar.gz) = 083f5e675d73f3233c7930ebe20425a533feedeaaa9d8cc86831312a6581cefbe6ed0d08d2fa89be81082f2a5abdabca8b3c080bf97218a1bd59dc118a30b9f3
-SHA512 (pcre-8.43.tar.bz2) = 3b4ac2c7ccd77c9575d07a33c3456f40b50731029e62d01fb8f2f5871d7118e12bc9e6bc7a8079769c765e38da5ecf98c4b261b10ff0a2f14f0881b434f67af7
-SHA512 (curl-7.67.0.tar.bz2) = 096e12be86bca1c19ba9e1d98b8342ec0d76b2e00cab322a7109d1e3559343ff7702b993c772f221fa073d2b8b6ffe6535d15411819fb245d3fa2c18e110b0a5
-SHA512 (R-3.6.3.tar.gz) = 9b1dc78922e431bd1af81e6e560b10ad04d121718f680fed32db735d561fd40ea6028759976722db11559f1a78fe684119b766f0567128cb2ee5003aa87a0931
+SHA512 (xz-5.2.5.tar.bz2) = 89e25ddf72427ee9608cbf2e9dbc24d592cb67a27f44ccf7d47e4d9405774444e9cfcd02ac4bcb92064860371ed31d3cfbecd5fe063f296ead607714c0a664a1
+SHA512 (R-4.0.3.tar.gz) = 2493295f3052d077a4820c0f84ca1c37df262b8b357f62f2ea99dbfffea065861735a08fa2098421078e58e917c540e680a668546d450af734722b421669e058
+SHA512 (pcre-8.44.tar.bz2) = f26d850aab5228799e58ac8c2306fb313889332c39e29b118ef1de57677c5c90f970d68d3f475cabc64f8b982a77f04eca990ff1057f3ccf5e19bd137997c4ac
+SHA512 (curl-7.72.0.tar.bz2) = ca787b8890c485f3176b9d51b024d217d69f28c34ab84c4091a2fcbbe5f13346efd559e9bb507971aec0ecb6ec4ed5975d2722773015728b72d3f26a3574c312