Merge branch 'f36' into f35

https://fedoraproject.org/wiki/Changes/Java17

.gitignore

@@ -41,3 +41,9 @@
 /R-4.0.3.tar.gz
 /pcre-8.44.tar.bz2
 /curl-7.72.0.tar.bz2
+/R-4.0.4.tar.gz
+/R-4.0.5.tar.gz
+/R-4.1.0.tar.gz
+/R-4.1.1.tar.gz
+/R-4.1.2.tar.gz
+/R-4.1.3.tar.gz

R.spec

@@ -1,8 +1,35 @@
 # We do not want this.
 %define __brp_mangle_shebangs /usr/bin/true
 
+# The additional linker flags break binary R- packages.
+# https://bugzilla.redhat.com/show_bug.cgi?id=2046246
+%undefine _package_note_flags
+
+# enabling LTO in Fedora 36 results in:
+# checking whether gfortran -m64 and gcc -m64 agree on double complex...
+# configure: WARNING: gfortran -m64 and gcc -m64 disagree on double
+# complex
+# AND that leads to
+#  Fortran complex functions are not available on this platform
+%if 0%{?fedora} >= 35 || 0%{?rhel} >= 9
+%global _lto_cflags %nil
+%endif
+
 %global runjavareconf 1
 
+%define javareconf() %{expand:
+%if %{runjavareconf}
+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/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}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \\
+    > /dev/null 2>&1 || exit 0
+%endif
+}
+
 # lapack comes from openblas, whenever possible.
 # 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
@@ -154,12 +181,12 @@
 %endif
 
 %global major_version 4
-%global minor_version 0
+%global minor_version 1
 %global patch_version 3
 
 Name: R
 Version: %{major_version}.%{minor_version}.%{patch_version}
-Release: 1%{?dist}
+Release: 2%{?dist}
 Summary: A language for data analysis and graphics
 URL: http://www.r-project.org
 Source0: https://cran.r-project.org/src/base/R-4/R-%{version}.tar.gz
@@ -188,6 +215,7 @@ Source1001: https://www.sourceware.org/pub/bzip2/bzip2-%{bzipv}.tar.gz
 Source1002: http://tukaani.org/xz/xz-%{xzv}.tar.bz2
 Source1003: https://ftp.pcre.org/pub/pcre/pcre-%{pcrev}.tar.bz2
 Source1004: https://curl.haxx.se/download/curl-%{curlv}.tar.bz2
+BuildRequires: make
 BuildRequires: glibc-devel
 BuildRequires: groff
 BuildRequires: krb5-libs
@@ -349,35 +377,35 @@ Provides: R(ABI) = %{major_version}.%{minor_version}
   local version = rpm.expand("%2")
   local rpm_version = string.gsub(version, "-", ".")
   print("Provides: R-" .. name .. " = " .. rpm_version .. "\\n")
-  print("Provides: R(" .. name .. ") = " .. version)
+  print("Provides: R(" .. name .. ") = " .. rpm_version)
 }
 %add_submodule base %{version}
-%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 boot 1.3-28
+%add_submodule class 7.3-20
+%add_submodule cluster 2.1.2
+%add_submodule codetools 0.2-18
 %add_submodule compiler %{version}
 %add_submodule datasets %{version}
-%add_submodule foreign 0.8-80
+%add_submodule foreign 0.8-82
 %add_submodule graphics %{version}
 %add_submodule grDevices %{version}
 %add_submodule grid %{version}
-%add_submodule KernSmooth 2.23-17
-%add_submodule lattice 0.20-41
-%add_submodule MASS 7.3-53
-%add_submodule Matrix 1.2-18
+%add_submodule KernSmooth 2.23-20
+%add_submodule lattice 0.20-45
+%add_submodule MASS 7.3-55
+%add_submodule Matrix 1.4-0
 Obsoletes: R-Matrix < 0.999375-7
 %add_submodule methods %{version}
-%add_submodule mgcv 1.8-33
-%add_submodule nlme 3.1-149
-%add_submodule nnet 7.3-14
+%add_submodule mgcv 1.8-39
+%add_submodule nlme 3.1-155
+%add_submodule nnet 7.3-17
 %add_submodule parallel %{version}
-%add_submodule rpart 4.1-15
-%add_submodule spatial 7.3-12
+%add_submodule rpart 4.1.16
+%add_submodule spatial 7.3-15
 %add_submodule splines %{version}
 %add_submodule stats %{version}
 %add_submodule stats4 %{version}
-%add_submodule survival 3.2-7
+%add_submodule survival 3.2-13
 %add_submodule tcltk %{version}
 %add_submodule tools %{version}
 %add_submodule translations %{version}
@@ -443,7 +471,7 @@ Requires: tex(cm-super-ts1.enc)
 Requires: qpdf
 %endif
 
-Provides: R-Matrix-devel = 1.2.18
+Provides: R-Matrix-devel = 1.4.0
 Obsoletes: R-Matrix-devel < 0.999375-7
 
 %if %{modern}
@@ -687,7 +715,7 @@ sed -i '/"checking whether the BLAS is complete/i r_cv_complete_blas=yes' config
 %endif
     --with-system-valgrind-headers \
 %if %{syslapack}
-    --with-lapack \
+    --with-lapack="flexiblas" \
 %if %{flexiblas}
     --with-blas="flexiblas" \
 %else
@@ -859,16 +887,6 @@ TZ="Europe/Paris" make check
 
 %post core
 /sbin/ldconfig
-%if %{runjavareconf}
-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/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}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
-    > /dev/null 2>&1 || exit 0
-%endif
 
 # With 2.10.0, we no longer need to do any of this.
 
@@ -889,32 +907,15 @@ if [ $1 -eq 0 ] ; then
 fi
 
 %posttrans core
+%{javareconf}
 /usr/bin/mktexlsr %{_datadir}/texmf &>/dev/null || :
 
 %if %{modern}
-%post java
-%if %{runjavareconf}
-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/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}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
-    > /dev/null 2>&1 || exit 0
-%endif
+%posttrans java
+%{javareconf}
 
-%post java-devel
-%if %{runjavareconf}
-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/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}:%{_jvmdir}/jre/lib/server:/usr/java/packages/lib/%{java_arch}:/lib:/usr/lib \
-    > /dev/null 2>&1 || exit 0
-%endif
+%posttrans java-devel
+%{javareconf}
 %endif
 
 %ldconfig_scriptlets -n libRmath
@@ -949,6 +950,7 @@ R CMD javareconf \
 %lang(it) %{_libdir}/R/library/translations/it/
 %lang(ja) %{_libdir}/R/library/translations/ja/
 %lang(ko) %{_libdir}/R/library/translations/ko/
+%lang(lt) %{_libdir}/R/library/translations/lt/
 %lang(nn) %{_libdir}/R/library/translations/nn/
 %lang(pl) %{_libdir}/R/library/translations/pl/
 %lang(pt) %{_libdir}/R/library/translations/pt*/
@@ -1014,7 +1016,9 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/cluster/po/de/
 %lang(en) %{_libdir}/R/library/cluster/po/en*/
 %lang(fr) %{_libdir}/R/library/cluster/po/fr/
+%lang(it) %{_libdir}/R/library/cluster/po/it/
 %lang(ko) %{_libdir}/R/library/cluster/po/ko/
+%lang(lt) %{_libdir}/R/library/cluster/po/lt/
 %lang(pl) %{_libdir}/R/library/cluster/po/pl/
 # codetools
 %dir %{_libdir}/R/library/codetools/
@@ -1087,6 +1091,7 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/lattice/po/de/
 %lang(en) %{_libdir}/R/library/lattice/po/en*/
 %lang(fr) %{_libdir}/R/library/lattice/po/fr/
+%lang(it) %{_libdir}/R/library/lattice/po/it/
 %lang(ko) %{_libdir}/R/library/lattice/po/ko/
 %lang(pl) %{_libdir}/R/library/lattice/po/pl*/
 %{_libdir}/R/library/lattice/R/
@@ -1132,7 +1137,9 @@ R CMD javareconf \
 %lang(de) %{_libdir}/R/library/Matrix/po/de/
 %lang(en) %{_libdir}/R/library/Matrix/po/en*/
 %lang(fr) %{_libdir}/R/library/Matrix/po/fr/
+%lang(it) %{_libdir}/R/library/Matrix/po/it/
 %lang(ko) %{_libdir}/R/library/Matrix/po/ko/
+%lang(lt) %{_libdir}/R/library/Matrix/po/lt/
 %lang(pl) %{_libdir}/R/library/Matrix/po/pl/
 %{_libdir}/R/library/Matrix/R/
 %{_libdir}/R/library/Matrix/test-tools.R
@@ -1280,6 +1287,52 @@ R CMD javareconf \
 %{_libdir}/libRmath.a
 
 %changelog
+* Fri Sep 23 2022 Iñaki Úcar <iucar@fedoraproject.org> - 4.1.3-2
+- Add flexiblas to LAPACK_LIBS
+
+* Sat Mar 19 2022 Tom Callaway <spot@fedoraproject.org> - 4.1.3-1
+- update to 4.1.3
+
+* Sat Feb 05 2022 Jiri Vanek <jvanek@redhat.com> - 4.1.2-4
+- Rebuilt for java-17-openjdk as system jdk
+
+* Wed Jan 26 2022 Tom Callaway <spot@fedoraproject.org> - 4.1.2-3
+- disable _package_note_flags because it breaks R modules
+
+* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 4.1.2-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Wed Nov  3 2021 Tom Callaway <spot@fedoraproject.org> - 4.1.2-1
+- update to 4.1.2
+
+* Fri Oct 29 2021 Iñaki Úcar <iucar@fedoraproject.org> - 4.1.1-2
+- Move javareconf to posttrans (bz 2009974)
+
+* Sat Aug 14 2021 Tom Callaway <spot@fedoraproject.org> - 4.1.1-1
+- update to 4.1.1
+
+* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 4.1.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Mon Jun  7 2021 Tom Callaway <spot@fedoraproject.org> - 4.1.0-1
+- update to 4.1.0
+
+* Wed May 19 2021 Pete Walter <pwalter@fedoraproject.org> - 4.0.5-2
+- Rebuild for ICU 69
+
+* Mon May  3 2021 Tom Callaway <spot@fedoraproject.org> - 4.0.5-1
+- update to 4.0.5
+
+* Mon Feb 15 2021 Tom Callaway <spot@fedoraproject.org> - 4.0.4-1
+- update to 4.0.4
+
+* Wed Feb 03 2021 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 4.0.3-3
+- Always provide normalized versions of R submodules
+- Fixes rhbz#1924565
+
+* Mon Jan 25 2021 Fedora Release Engineering <releng@fedoraproject.org> - 4.0.3-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
 * Mon Oct 12 2020 Tom Callaway <spot@fedoraproject.org> - 4.0.3-1
 - update to 4.0.3
 

package.cfg

@@ -1,2 +0,0 @@
-[koji]
-targets = epel8 epel8-playground

sources

@@ -1,6 +1,6 @@
 SHA512 (zlib-1.2.11.tar.gz) = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
 SHA512 (bzip2-1.0.8.tar.gz) = 083f5e675d73f3233c7930ebe20425a533feedeaaa9d8cc86831312a6581cefbe6ed0d08d2fa89be81082f2a5abdabca8b3c080bf97218a1bd59dc118a30b9f3
 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
+SHA512 (R-4.1.3.tar.gz) = cb71cc6c9551cc9cef4819ed778a8d0ef40490ec2bed27669c8e93d464a93bef5e73c2a03a714db03c87112b291a752ec2d21194e5abef81d85cb6c62643127c