Update sources

Even when built in /app for flatpaks, modules in the /usr prefix must also
be found, and a /usr/bin/Rscript symlink is needed to resolve shebang
dependencies when building other packages.

.gitignore

@@ -50,3 +50,14 @@
 /R-4.2.1.tar.gz
 /R-4.2.2.tar.gz
 /R-4.2.3.tar.gz
+/R-4.3.0.tar.gz
+/R-4.3.1.tar.gz
+/R-4.3.2.tar.gz
+/R-4.3.3.tar.gz
+/R-4.4.0.tar.gz
+/R-4.4.1.tar.gz
+/R-4.4.2.tar.gz
+/R-4.4.3.tar.gz
+/R-4.5.0.tar.gz
+/R-4.5.1.tar.gz
+/R-4.5.2.tar.gz

R.spec

@@ -1,5 +1,5 @@
-# We do not want this (we need +x on files in %%{_libdir}/R/bin/)
-%define __brp_mangle_shebangs /usr/bin/true
+# We need +x on these files
+%global __brp_mangle_shebangs_exclude_from %{_libdir}/R/bin/
 
 # The additional linker flags break binary R- packages
 # https://bugzilla.redhat.com/show_bug.cgi?id=2046246
@@ -12,18 +12,8 @@
 %bcond_without tests
 %endif
 
-# Using LTO breaks debuginfo (probably not true anymore?)
-# https://bugzilla.redhat.com/show_bug.cgi?id=1113404
-# Also, enabling LTO in Fedora 36 results in:
-# checking whether gfortran and gcc agree on double complex...
-# configure: WARNING: gfortran and gcc disagree on double complex
-# AND that leads to Fortran complex functions are not available on this platform
-%bcond_with lto
-
-# We need at least gcc 10 anyway
-%global enable_lto 1
-%if %{without lto} || (0%{?rhel} && 0%{?rhel} < 9)
-%global enable_lto 0
+# We need at least gcc 10
+%if 0%{?rhel} && 0%{?rhel} < 9
 %global _lto_cflags %nil
 %endif
 
@@ -35,9 +25,13 @@
 %global blasvar o
 %endif
 
+# Should be the previous version, to make mass-rebuilds easier
+%bcond_with bootstrap
+%global bootstrap_abi 4.4
+
 %global major_version 4
-%global minor_version 2
-%global patch_version 3
+%global minor_version 5
+%global patch_version 2
 
 Name:           R
 Version:        %{major_version}.%{minor_version}.%{patch_version}
@@ -66,6 +60,8 @@ BuildRequires:  libcurl-devel
 BuildRequires:  bzip2-devel
 BuildRequires:  xz-devel
 BuildRequires:  zlib-devel
+BuildRequires:  libdeflate-devel
+BuildRequires:  libzstd-devel
 BuildRequires:  tre-devel
 BuildRequires:  %{blaslib}-devel
 BuildRequires:  libSM-devel
@@ -74,6 +70,7 @@ BuildRequires:  libICE-devel
 BuildRequires:  libXt-devel
 BuildRequires:  libXmu-devel
 BuildRequires:  libicu-devel
+BuildRequires:  libtirpc-devel
 %ifarch %{valgrind_arches}
 BuildRequires:  valgrind-devel
 %endif
@@ -115,24 +112,10 @@ and called at run time.
 %package core
 Summary:        The minimal R components necessary for a functional runtime
 Requires:       libRmath%{?_isa} = %{version}-%{release}
-Requires:       xdg-utils
-# Bugzilla 1875165
-Recommends:     cups
-# R inherits the compiler flags it was built with, hence we need this on hardened systems
-Requires:       redhat-rpm-config
-Requires:       vi
-%if 0%{?fedora}
-Requires:       perl-interpreter
-%else
-Requires:       perl
-%endif
-Requires:       sed
-Requires:       gawk
-Requires:       tex(latex)
-Requires:       tex(dvips)
+Requires:       tzdata
 Requires:       less
-Requires:       make
-Requires:       unzip
+Requires:       xdg-utils
+Requires:       zip, unzip
 
 %ifnarch %{java_arches}
 Provides:       R-java = %{version}-%{release}
@@ -142,6 +125,9 @@ Obsoletes:      R-java < 4.1.3-3
 # 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}
+%if %{with bootstrap}
+Provides:       R(ABI) = %{bootstrap_abi}
+%endif
 
 # 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
@@ -154,32 +140,32 @@ Provides:       R(ABI) = %{major_version}.%{minor_version}
   print("Provides: R(" .. name .. ") = " .. rpm_version)
 }
 %add_submodule  base %{version}
-%add_submodule  boot 1.3-28
-%add_submodule  class 7.3-21
-%add_submodule  cluster 2.1.4
-%add_submodule  codetools 0.2-19
+%add_submodule  boot 1.3-32
+%add_submodule  class 7.3-23
+%add_submodule  cluster 2.1.8.1
+%add_submodule  codetools 0.2-20
 %add_submodule  compiler %{version}
 %add_submodule  datasets %{version}
-%add_submodule  foreign 0.8-84
+%add_submodule  foreign 0.8-90
 %add_submodule  graphics %{version}
 %add_submodule  grDevices %{version}
 %add_submodule  grid %{version}
-%add_submodule  KernSmooth 2.23-20
-%add_submodule  lattice 0.20-45
-%add_submodule  MASS 7.3-58.2
-%add_submodule  Matrix 1.5-3
+%add_submodule  KernSmooth 2.23-26
+%add_submodule  lattice 0.22-7
+%add_submodule  MASS 7.3-65
+%add_submodule  Matrix 1.7-4
 Obsoletes:      R-Matrix < 0.999375-7
 %add_submodule  methods %{version}
-%add_submodule  mgcv 1.8-42
-%add_submodule  nlme 3.1-162
-%add_submodule  nnet 7.3-18
+%add_submodule  mgcv 1.9-3
+%add_submodule  nlme 3.1-168
+%add_submodule  nnet 7.3-20
 %add_submodule  parallel %{version}
-%add_submodule  rpart 4.1.19
-%add_submodule  spatial 7.3-16
+%add_submodule  rpart 4.1.24
+%add_submodule  spatial 7.3-18
 %add_submodule  splines %{version}
 %add_submodule  stats %{version}
 %add_submodule  stats4 %{version}
-%add_submodule  survival 3.5-3
+%add_submodule  survival 3.8-3
 %add_submodule  tcltk %{version}
 %add_submodule  tools %{version}
 %add_submodule  translations %{version}
@@ -203,39 +189,37 @@ and called at run time.
 Summary:        Core files for development of R packages (no Java)
 Requires:       R-core%{?_isa} = %{version}-%{release}
 Requires:       libRmath-devel%{?_isa} = %{version}-%{release}
+# R inherits the compiler flags it was built with, hence we need this on hardened systems
+Requires:       redhat-rpm-config
 # You need all the BuildRequires for the development version
 Requires:       gcc-gfortran
 Requires:       gcc-c++
+Requires:       make
 Requires:       pkgconfig
-Requires:       tcl-devel
-Requires:       tk-devel
 Requires:       pcre2-devel
 Requires:       bzip2-devel
 Requires:       xz-devel
 Requires:       zlib-devel
+Requires:       libdeflate-devel
+Requires:       libzstd-devel
 Requires:       tre-devel
 Requires:       %{blaslib}-devel
 Requires:       libX11-devel
 Requires:       libicu-devel
-Requires:       tex(latex)
-Requires:       texinfo-tex
-Requires:       tex(ecrm1000.tfm)
-Requires:       tex(ptmr8t.tfm)
-Requires:       tex(ptmb8t.tfm)
-Requires:       tex(pcrr8t.tfm)
-Requires:       tex(phvr8t.tfm)
-Requires:       tex(ptmri8t.tfm)
-Requires:       tex(ptmro8t.tfm)
-Requires:       tex(cm-super-ts1.enc)
+Requires:       libtirpc-devel
+Recommends:     tex(latex)
+Recommends:     texinfo-tex
+Recommends:     tidy
+Recommends:     devscripts-checkbashisms
 %if 0%{?fedora}
 # No inconsolata on RHEL tex
-Requires:       tex(inconsolata.sty)
+Recommends:     tex(inconsolata.sty)
 # "‘qpdf’ is needed for checks on size reduction of PDFs"
 # qpdf is not in epel, and since 99% of R doesn't use it, we'll let it slide.
-Requires:       qpdf
+Recommends:     qpdf
 %endif
 
-Provides:       R-Matrix-devel = 1.5.3
+Provides:       R-Matrix-devel = 1.7.4
 Obsoletes:      R-Matrix-devel < 0.999375-7
 
 %ifarch %{java_arches}
@@ -323,38 +307,22 @@ from the R project.  This package provides the static libRmath library.
 
 %prep
 %setup -q
-%patch0 -p1 -b .fixpath
-
-# Filter false positive provides.
-cat <<EOF > %{name}-prov
-#!/bin/sh
-%{__perl_provides} \
-| grep -v 'File::Copy::Recursive' | grep -v 'Text::DelimMatch'
-EOF
-
-%global __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
-%global __perl_requires %{_builddir}/R-%{version}/%{name}-req
-chmod +x %{__perl_requires}
+%patch -P0 -p1 -b .fixpath
+# A bunch of macOS stuff in v4.5.2's archive
+find . -name '._*' -delete
 
 %build
 # Comment out default R_LIBS_SITE (since R 4.2) and set our own as always
 sed -i -e '/R_LIBS_SITE=/s/^/#/g' etc/Renviron.in
-echo 'R_LIBS_SITE=${R_LIBS_SITE-'"'/usr/local/lib/R/site-library:/usr/local/lib/R/library:%{_libdir}/R/library:%{_datadir}/R/library'"'}' >> etc/Renviron.in
+# Only packages which are needed as runtime dependencies are rebuilt for
+# flatpaks in /app, build dependencies are from buildroot in /usr
+echo 'R_LIBS_SITE=${R_LIBS_SITE-'"'/usr/local/lib/R/site-library:/usr/local/lib/R/library:%{_libdir}/R/library:%{_datadir}/R/library%{?flatpak::/usr/%{_lib}/R/library:/usr/share/R/library}'"'}' >> etc/Renviron.in
 # No inconsolata on RHEL tex
 %if 0%{?rhel}
 export R_RD4PDF="times,hyper"
 sed -i 's|inconsolata,||g' etc/Renviron.in
 %endif
 export R_PDFVIEWER="%{_bindir}/xdg-open"
-export R_PRINTCMD="lpr"
 export R_BROWSER="%{_bindir}/xdg-open"
 
 %ifarch %{java_arches}
@@ -366,20 +334,14 @@ export JAVA_HOME=%{_jvmdir}/jre
   rincludedir=%{_includedir}/R \
   rsharedir=%{_datadir}/R \
   --with-system-tre \
-%ifarch %{valgrind_arches}
-  --with-system-valgrind-headers \
-%endif
-  --with-lapack=%{blaslib}%{blasvar} \
   --with-blas=%{blaslib}%{blasvar} \
-  --with-tcl-config=%{_libdir}/tclConfig.sh \
-  --with-tk-config=%{_libdir}/tkConfig.sh \
+  --with-lapack \
+  --with-tcl-config=/usr/%{_lib}/tclConfig.sh \
+  --with-tk-config=/usr/%{_lib}/tkConfig.sh \
   --enable-R-shlib \
   --enable-prebuilt-html \
   --enable-R-profiling \
   --enable-memory-profiling \
-%if %{enable_lto}
-  --enable-lto \
-%endif
   | tee CONFIGURE.log
 cat CONFIGURE.log | grep -A30 'R is now' - > CAPABILITIES
 make V=1
@@ -404,8 +366,8 @@ install -p CAPABILITIES %{buildroot}%{_pkgdocdir}
 # Install libRmath files
 (cd src/nmath/standalone; make install DESTDIR=%{buildroot})
 
-mkdir -p %{buildroot}/etc/ld.so.conf.d
-echo "%{_libdir}/R/lib" > %{buildroot}/etc/ld.so.conf.d/%{name}-%{_arch}.conf
+mkdir -p %{buildroot}%{_sysconfdir}/ld.so.conf.d
+echo "%{_libdir}/R/lib" > %{buildroot}%{_sysconfdir}/ld.so.conf.d/%{name}-%{_arch}.conf
 
 mkdir -p %{buildroot}%{_datadir}/R/library
 
@@ -435,12 +397,18 @@ if [ ! -d "%{buildroot}%{_libdir}/R/include" ]; then
 fi
 
 # Symbolic link for LaTeX
-if [ ! -d "%{buildroot}%{_datadir}/texmf/tex/latex/R" ]; then
-	mkdir -p %{buildroot}%{_datadir}/texmf/tex/latex
-	pushd %{buildroot}%{_datadir}/texmf/tex/latex
-	ln -s %{_datadir}/R/texmf/tex/latex R
-	popd
-fi
+%{!?_texdir:  %global _texdir  %{_datadir}/texlive}
+%{!?_texdist: %global _texdist %{_texdir}/texmf-dist}
+for i in tex/latex bibtex/bib bibtex/bst; do
+  mkdir -p %{buildroot}%{_texdist}/$i
+  (cd %{buildroot}%{_texdist}/$i && ln -s %{_datadir}/R/texmf/$i R)
+done
+
+%if 0%{?flatpak}
+# keep compatibility with shebang dependencies
+mkdir -p %{buildroot}/usr/bin
+ln -s /app/bin/Rscript %{buildroot}/usr/bin/Rscript
+%endif
 
 %check
 %if %{with tests}
@@ -450,20 +418,6 @@ ulimit -s 16384
 TZ="Europe/Paris" make check
 %endif
 
-%post core
-/sbin/ldconfig
-
-%postun core
-/sbin/ldconfig
-if [ $1 -eq 0 ] ; then
-    /usr/bin/mktexlsr %{_datadir}/texmf &>/dev/null || :
-fi
-
-%posttrans core
-/usr/bin/mktexlsr %{_datadir}/texmf &>/dev/null || :
-
-%ldconfig_scriptlets -n libRmath
-
 %files
 # Metapackage
 
@@ -471,7 +425,17 @@ fi
 %{_bindir}/R
 %{_bindir}/Rscript
 %{_datadir}/R/
-%{_datadir}/texmf/tex/latex/R
+# Links to LaTeX stuff
+%dir %{_texdir}
+%dir %{_texdist}
+%dir %{_texdist}/tex/
+%dir %{_texdist}/tex/latex/
+%{_texdist}/tex/latex/R
+%dir %{_texdist}/bibtex/
+%dir %{_texdist}/bibtex/bib/
+%{_texdist}/bibtex/bib/R
+%dir %{_texdist}/bibtex/bst/
+%{_texdist}/bibtex/bst/R
 # Have to break this out for the translations
 %dir %{_libdir}/R/
 %{_libdir}/R/bin/
@@ -485,24 +449,41 @@ fi
 %dir %{_libdir}/R/library/
 %dir %{_libdir}/R/library/translations/
 %{_libdir}/R/library/translations/DESCRIPTION
+%lang(ar) %{_libdir}/R/library/translations/ar/
+%lang(bn) %{_libdir}/R/library/translations/bn/
+%lang(ca) %{_libdir}/R/library/translations/ca/
 %lang(da) %{_libdir}/R/library/translations/da/
 %lang(de) %{_libdir}/R/library/translations/de/
 %lang(en) %{_libdir}/R/library/translations/en*/
 %lang(es) %{_libdir}/R/library/translations/es/
 %lang(fa) %{_libdir}/R/library/translations/fa/
 %lang(fr) %{_libdir}/R/library/translations/fr/
+%lang(hi) %{_libdir}/R/library/translations/hi/
+%lang(hu) %{_libdir}/R/library/translations/hu/
+%lang(id) %{_libdir}/R/library/translations/id/
 %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(ne) %{_libdir}/R/library/translations/ne/
 %lang(nn) %{_libdir}/R/library/translations/nn/
 %lang(pl) %{_libdir}/R/library/translations/pl/
 %lang(pt) %{_libdir}/R/library/translations/pt*/
 %lang(ru) %{_libdir}/R/library/translations/ru/
+%lang(sq) %{_libdir}/R/library/translations/sq/
 %lang(tr) %{_libdir}/R/library/translations/tr/
+%lang(ur) %{_libdir}/R/library/translations/ur/
 %lang(zh) %{_libdir}/R/library/translations/zh*/
 # base
-%{_libdir}/R/library/base/
+%dir %{_libdir}/R/library/base/
+%{_libdir}/R/library/base/CITATION
+%{_libdir}/R/library/base/demo/
+%{_libdir}/R/library/base/DESCRIPTION
+%{_libdir}/R/library/base/help/
+%doc %{_libdir}/R/library/base/html/
+%{_libdir}/R/library/base/INDEX
+%{_libdir}/R/library/base/Meta/
+%{_libdir}/R/library/base/R/
 # boot
 %dir %{_libdir}/R/library/boot/
 %{_libdir}/R/library/boot/bd.q
@@ -510,7 +491,7 @@ fi
 %{_libdir}/R/library/boot/data/
 %{_libdir}/R/library/boot/DESCRIPTION
 %{_libdir}/R/library/boot/help/
-%{_libdir}/R/library/boot/html/
+%doc %{_libdir}/R/library/boot/html/
 %{_libdir}/R/library/boot/INDEX
 %{_libdir}/R/library/boot/Meta/
 %{_libdir}/R/library/boot/NAMESPACE
@@ -528,12 +509,12 @@ fi
 %{_libdir}/R/library/class/CITATION
 %{_libdir}/R/library/class/DESCRIPTION
 %{_libdir}/R/library/class/help/
-%{_libdir}/R/library/class/html/
+%doc %{_libdir}/R/library/class/html/
 %{_libdir}/R/library/class/INDEX
 %{_libdir}/R/library/class/libs/
 %{_libdir}/R/library/class/Meta/
 %{_libdir}/R/library/class/NAMESPACE
-%{_libdir}/R/library/class/NEWS
+%doc %{_libdir}/R/library/class/NEWS
 %dir %{_libdir}/R/library/class/po/
 %lang(de) %{_libdir}/R/library/class/po/de/
 %lang(en) %{_libdir}/R/library/class/po/en*/
@@ -548,14 +529,12 @@ fi
 %{_libdir}/R/library/cluster/data/
 %{_libdir}/R/library/cluster/DESCRIPTION
 %{_libdir}/R/library/cluster/help/
-%{_libdir}/R/library/cluster/html/
+%doc %{_libdir}/R/library/cluster/html/
 %{_libdir}/R/library/cluster/INDEX
 %{_libdir}/R/library/cluster/libs/
 %{_libdir}/R/library/cluster/Meta/
 %{_libdir}/R/library/cluster/NAMESPACE
-%{_libdir}/R/library/cluster/NEWS.Rd
-%{_libdir}/R/library/cluster/R/
-%{_libdir}/R/library/cluster/test-tools.R
+%doc %{_libdir}/R/library/cluster/NEWS.Rd
 %dir %{_libdir}/R/library/cluster/po/
 %lang(de) %{_libdir}/R/library/cluster/po/de/
 %lang(en) %{_libdir}/R/library/cluster/po/en*/
@@ -564,26 +543,42 @@ fi
 %lang(ko) %{_libdir}/R/library/cluster/po/ko/
 %lang(lt) %{_libdir}/R/library/cluster/po/lt/
 %lang(pl) %{_libdir}/R/library/cluster/po/pl/
+%{_libdir}/R/library/cluster/R/
+%{_libdir}/R/library/cluster/test-tools.R
 # codetools
 %dir %{_libdir}/R/library/codetools/
 %{_libdir}/R/library/codetools/DESCRIPTION
 %{_libdir}/R/library/codetools/help/
-%{_libdir}/R/library/codetools/html/
+%doc %{_libdir}/R/library/codetools/html/
 %{_libdir}/R/library/codetools/INDEX
 %{_libdir}/R/library/codetools/Meta/
 %{_libdir}/R/library/codetools/NAMESPACE
 %{_libdir}/R/library/codetools/R/
 # compiler
-%{_libdir}/R/library/compiler/
+%dir %{_libdir}/R/library/compiler/
+%{_libdir}/R/library/compiler/DESCRIPTION
+%{_libdir}/R/library/compiler/help/
+%doc %{_libdir}/R/library/compiler/html/
+%{_libdir}/R/library/compiler/INDEX
+%{_libdir}/R/library/compiler/Meta/
+%{_libdir}/R/library/compiler/NAMESPACE
+%{_libdir}/R/library/compiler/R/
 # datasets
-%{_libdir}/R/library/datasets/
+%dir %{_libdir}/R/library/datasets/
+%{_libdir}/R/library/datasets/data/
+%{_libdir}/R/library/datasets/DESCRIPTION
+%{_libdir}/R/library/datasets/help/
+%doc %{_libdir}/R/library/datasets/html
+%{_libdir}/R/library/datasets/INDEX
+%{_libdir}/R/library/datasets/Meta/
+%{_libdir}/R/library/datasets/NAMESPACE
 # foreign
 %dir %{_libdir}/R/library/foreign/
-%{_libdir}/R/library/foreign/COPYRIGHTS
+%license %{_libdir}/R/library/foreign/COPYRIGHTS
 %{_libdir}/R/library/foreign/DESCRIPTION
 %{_libdir}/R/library/foreign/files/
 %{_libdir}/R/library/foreign/help/
-%{_libdir}/R/library/foreign/html/
+%doc %{_libdir}/R/library/foreign/html/
 %{_libdir}/R/library/foreign/INDEX
 %{_libdir}/R/library/foreign/libs/
 %{_libdir}/R/library/foreign/Meta/
@@ -596,16 +591,47 @@ fi
 %lang(pl) %{_libdir}/R/library/foreign/po/pl/
 %{_libdir}/R/library/foreign/R/
 # graphics
-%{_libdir}/R/library/graphics/
+%dir %{_libdir}/R/library/graphics/
+%{_libdir}/R/library/graphics/demo/
+%{_libdir}/R/library/graphics/DESCRIPTION
+%{_libdir}/R/library/graphics/help/
+%doc %{_libdir}/R/library/graphics/html/
+%{_libdir}/R/library/graphics/INDEX
+%{_libdir}/R/library/graphics/libs/
+%{_libdir}/R/library/graphics/Meta/
+%{_libdir}/R/library/graphics/NAMESPACE
+%{_libdir}/R/library/graphics/R/
 # grDevices
-%{_libdir}/R/library/grDevices
+%dir %{_libdir}/R/library/grDevices/
+%{_libdir}/R/library/grDevices/afm/
+%{_libdir}/R/library/grDevices/demo/
+%{_libdir}/R/library/grDevices/DESCRIPTION
+%{_libdir}/R/library/grDevices/enc/
+%{_libdir}/R/library/grDevices/fonts/
+%{_libdir}/R/library/grDevices/help/
+%doc %{_libdir}/R/library/grDevices/html/
+%{_libdir}/R/library/grDevices/icc/
+%{_libdir}/R/library/grDevices/INDEX
+%{_libdir}/R/library/grDevices/libs/
+%{_libdir}/R/library/grDevices/Meta/
+%{_libdir}/R/library/grDevices/NAMESPACE
+%{_libdir}/R/library/grDevices/R/
 # grid
-%{_libdir}/R/library/grid/
+%dir %{_libdir}/R/library/grid/
+%{_libdir}/R/library/grid/DESCRIPTION
+%doc %{_libdir}/R/library/grid/doc/
+%{_libdir}/R/library/grid/help/
+%doc %{_libdir}/R/library/grid/html/
+%{_libdir}/R/library/grid/INDEX
+%{_libdir}/R/library/grid/libs/
+%{_libdir}/R/library/grid/Meta/
+%{_libdir}/R/library/grid/NAMESPACE
+%{_libdir}/R/library/grid/R/
 # KernSmooth
 %dir %{_libdir}/R/library/KernSmooth/
 %{_libdir}/R/library/KernSmooth/DESCRIPTION
 %{_libdir}/R/library/KernSmooth/help/
-%{_libdir}/R/library/KernSmooth/html/
+%doc %{_libdir}/R/library/KernSmooth/html/
 %{_libdir}/R/library/KernSmooth/INDEX
 %{_libdir}/R/library/KernSmooth/libs/
 %{_libdir}/R/library/KernSmooth/Meta/
@@ -624,13 +650,14 @@ fi
 %{_libdir}/R/library/lattice/data/
 %{_libdir}/R/library/lattice/demo/
 %{_libdir}/R/library/lattice/DESCRIPTION
+%doc %{_libdir}/R/library/lattice/doc/
 %{_libdir}/R/library/lattice/help/
-%{_libdir}/R/library/lattice/html/
+%doc %{_libdir}/R/library/lattice/html/
 %{_libdir}/R/library/lattice/INDEX
 %{_libdir}/R/library/lattice/libs/
 %{_libdir}/R/library/lattice/Meta/
 %{_libdir}/R/library/lattice/NAMESPACE
-%{_libdir}/R/library/lattice/NEWS
+%doc %{_libdir}/R/library/lattice/NEWS.md
 %dir %{_libdir}/R/library/lattice/po/
 %lang(de) %{_libdir}/R/library/lattice/po/de/
 %lang(en) %{_libdir}/R/library/lattice/po/en*/
@@ -645,12 +672,12 @@ fi
 %{_libdir}/R/library/MASS/data/
 %{_libdir}/R/library/MASS/DESCRIPTION
 %{_libdir}/R/library/MASS/help/
-%{_libdir}/R/library/MASS/html/
+%doc %{_libdir}/R/library/MASS/html/
 %{_libdir}/R/library/MASS/INDEX
 %{_libdir}/R/library/MASS/libs/
 %{_libdir}/R/library/MASS/Meta/
 %{_libdir}/R/library/MASS/NAMESPACE
-%{_libdir}/R/library/MASS/NEWS
+%doc %{_libdir}/R/library/MASS/NEWS
 %dir %{_libdir}/R/library/MASS/po
 %lang(de) %{_libdir}/R/library/MASS/po/de/
 %lang(en) %{_libdir}/R/library/MASS/po/en*/
@@ -662,21 +689,19 @@ fi
 %{_libdir}/R/library/MASS/scripts/
 # Matrix
 %dir %{_libdir}/R/library/Matrix/
-%{_libdir}/R/library/Matrix/Copyrights
 %{_libdir}/R/library/Matrix/data/
-%{_libdir}/R/library/Matrix/doc/
 %{_libdir}/R/library/Matrix/DESCRIPTION
-%{_libdir}/R/library/Matrix/Doxyfile
+%doc %{_libdir}/R/library/Matrix/doc/
 %{_libdir}/R/library/Matrix/external/
 %{_libdir}/R/library/Matrix/help/
-%{_libdir}/R/library/Matrix/html/
+%doc %{_libdir}/R/library/Matrix/html/
 %{_libdir}/R/library/Matrix/include/
 %{_libdir}/R/library/Matrix/INDEX
 %{_libdir}/R/library/Matrix/libs/
-%{_libdir}/R/library/Matrix/LICENCE
+%license %{_libdir}/R/library/Matrix/LICENCE
 %{_libdir}/R/library/Matrix/Meta/
 %{_libdir}/R/library/Matrix/NAMESPACE
-%{_libdir}/R/library/Matrix/NEWS.Rd
+%doc %{_libdir}/R/library/Matrix/NEWS.Rd
 %dir %{_libdir}/R/library/Matrix/po/
 %lang(de) %{_libdir}/R/library/Matrix/po/de/
 %lang(en) %{_libdir}/R/library/Matrix/po/en*/
@@ -686,20 +711,45 @@ fi
 %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/scripts/
 %{_libdir}/R/library/Matrix/test-tools.R
 %{_libdir}/R/library/Matrix/test-tools-1.R
 %{_libdir}/R/library/Matrix/test-tools-Matrix.R
 # methods
-%{_libdir}/R/library/methods/
+%dir %{_libdir}/R/library/methods/
+%{_libdir}/R/library/methods/DESCRIPTION
+%{_libdir}/R/library/methods/help/
+%doc %{_libdir}/R/library/methods/html/
+%{_libdir}/R/library/methods/INDEX
+%{_libdir}/R/library/methods/libs/
+%{_libdir}/R/library/methods/Meta/
+%{_libdir}/R/library/methods/NAMESPACE
+%{_libdir}/R/library/methods/R/
 # mgcv
-%{_libdir}/R/library/mgcv/
+%dir %{_libdir}/R/library/mgcv/
+%{_libdir}/R/library/mgcv/CITATION
+%{_libdir}/R/library/mgcv/data/
+%{_libdir}/R/library/mgcv/DESCRIPTION
+%{_libdir}/R/library/mgcv/help/
+%doc %{_libdir}/R/library/mgcv/html/
+%{_libdir}/R/library/mgcv/INDEX
+%{_libdir}/R/library/mgcv/libs/
+%{_libdir}/R/library/mgcv/Meta/
+%{_libdir}/R/library/mgcv/NAMESPACE
+%dir %{_libdir}/R/library/mgcv/po/
+%lang(de) %{_libdir}/R/library/mgcv/po/de/
+%lang(en) %{_libdir}/R/library/mgcv/po/en*/
+%lang(fr) %{_libdir}/R/library/mgcv/po/fr/
+%lang(ko) %{_libdir}/R/library/mgcv/po/ko/
+%lang(pl) %{_libdir}/R/library/mgcv/po/pl/
+%{_libdir}/R/library/mgcv/R/
 # nlme
 %dir %{_libdir}/R/library/nlme/
 %{_libdir}/R/library/nlme/CITATION
 %{_libdir}/R/library/nlme/data/
 %{_libdir}/R/library/nlme/DESCRIPTION
 %{_libdir}/R/library/nlme/help/
-%{_libdir}/R/library/nlme/html/
+%doc %{_libdir}/R/library/nlme/html/
 %{_libdir}/R/library/nlme/INDEX
 %{_libdir}/R/library/nlme/libs/
 %{_libdir}/R/library/nlme/Meta/
@@ -718,12 +768,12 @@ fi
 %{_libdir}/R/library/nnet/CITATION
 %{_libdir}/R/library/nnet/DESCRIPTION
 %{_libdir}/R/library/nnet/help/
-%{_libdir}/R/library/nnet/html/
+%doc %{_libdir}/R/library/nnet/html/
 %{_libdir}/R/library/nnet/INDEX
 %{_libdir}/R/library/nnet/libs/
 %{_libdir}/R/library/nnet/Meta/
 %{_libdir}/R/library/nnet/NAMESPACE
-%{_libdir}/R/library/nnet/NEWS
+%doc %{_libdir}/R/library/nnet/NEWS
 %dir %{_libdir}/R/library/nnet/po
 %lang(de) %{_libdir}/R/library/nnet/po/de/
 %lang(en) %{_libdir}/R/library/nnet/po/en*/
@@ -733,19 +783,28 @@ fi
 %lang(pl) %{_libdir}/R/library/nnet/po/pl/
 %{_libdir}/R/library/nnet/R/
 # parallel
-%{_libdir}/R/library/parallel/
+%dir %{_libdir}/R/library/parallel/
+%{_libdir}/R/library/parallel/DESCRIPTION
+%doc %{_libdir}/R/library/parallel/doc/
+%{_libdir}/R/library/parallel/help/
+%doc %{_libdir}/R/library/parallel/html/
+%{_libdir}/R/library/parallel/INDEX
+%{_libdir}/R/library/parallel/libs/
+%{_libdir}/R/library/parallel/Meta/
+%{_libdir}/R/library/parallel/NAMESPACE
+%{_libdir}/R/library/parallel/R/
 # rpart
 %dir %{_libdir}/R/library/rpart/
 %{_libdir}/R/library/rpart/data/
 %{_libdir}/R/library/rpart/DESCRIPTION
-%{_libdir}/R/library/rpart/doc/
+%doc %{_libdir}/R/library/rpart/doc/
 %{_libdir}/R/library/rpart/help/
-%{_libdir}/R/library/rpart/html/
+%doc %{_libdir}/R/library/rpart/html/
 %{_libdir}/R/library/rpart/INDEX
 %{_libdir}/R/library/rpart/libs/
 %{_libdir}/R/library/rpart/Meta/
 %{_libdir}/R/library/rpart/NAMESPACE
-%{_libdir}/R/library/rpart/NEWS.Rd
+%doc %{_libdir}/R/library/rpart/NEWS.Rd
 %dir %{_libdir}/R/library/rpart/po
 %lang(de) %{_libdir}/R/library/rpart/po/de/
 %lang(en) %{_libdir}/R/library/rpart/po/en*/
@@ -759,12 +818,12 @@ fi
 %{_libdir}/R/library/spatial/CITATION
 %{_libdir}/R/library/spatial/DESCRIPTION
 %{_libdir}/R/library/spatial/help/
-%{_libdir}/R/library/spatial/html/
+%doc %{_libdir}/R/library/spatial/html/
 %{_libdir}/R/library/spatial/INDEX
 %{_libdir}/R/library/spatial/libs/
 %{_libdir}/R/library/spatial/Meta/
 %{_libdir}/R/library/spatial/NAMESPACE
-%{_libdir}/R/library/spatial/NEWS
+%doc %{_libdir}/R/library/spatial/NEWS
 %dir %{_libdir}/R/library/spatial/po
 %lang(de) %{_libdir}/R/library/spatial/po/de/
 %lang(en) %{_libdir}/R/library/spatial/po/en*/
@@ -776,28 +835,103 @@ fi
 %{_libdir}/R/library/spatial/PP.files
 %{_libdir}/R/library/spatial/R/
 # splines
-%{_libdir}/R/library/splines/
+%dir %{_libdir}/R/library/splines/
+%{_libdir}/R/library/splines/DESCRIPTION
+%{_libdir}/R/library/splines/help/
+%doc %{_libdir}/R/library/splines/html/
+%{_libdir}/R/library/splines/INDEX
+%{_libdir}/R/library/splines/libs/
+%{_libdir}/R/library/splines/Meta/
+%{_libdir}/R/library/splines/NAMESPACE
+%{_libdir}/R/library/splines/R/
 # stats
-%{_libdir}/R/library/stats/
+%dir %{_libdir}/R/library/stats/
+%license %{_libdir}/R/library/stats/COPYRIGHTS.modreg
+%{_libdir}/R/library/stats/demo/
+%{_libdir}/R/library/stats/DESCRIPTION
+%doc %{_libdir}/R/library/stats/doc/
+%{_libdir}/R/library/stats/help/
+%doc %{_libdir}/R/library/stats/html/
+%{_libdir}/R/library/stats/INDEX
+%{_libdir}/R/library/stats/libs/
+%{_libdir}/R/library/stats/Meta/
+%{_libdir}/R/library/stats/NAMESPACE
+%{_libdir}/R/library/stats/R/
+%{_libdir}/R/library/stats/SOURCES.ts
 # stats4
-%{_libdir}/R/library/stats4/
+%dir %{_libdir}/R/library/stats4/
+%{_libdir}/R/library/stats4/DESCRIPTION
+%{_libdir}/R/library/stats4/help/
+%doc %{_libdir}/R/library/stats4/html/
+%{_libdir}/R/library/stats4/INDEX
+%{_libdir}/R/library/stats4/Meta/
+%{_libdir}/R/library/stats4/NAMESPACE
+%{_libdir}/R/library/stats4/R/
 # survival
-%{_libdir}/R/library/survival/
+%dir %{_libdir}/R/library/survival/
+%{_libdir}/R/library/survival/CITATION
+%license %{_libdir}/R/library/survival/COPYRIGHTS
+%{_libdir}/R/library/survival/data/
+%{_libdir}/R/library/survival/DESCRIPTION
+%doc %{_libdir}/R/library/survival/doc/
+%{_libdir}/R/library/survival/help
+%doc %{_libdir}/R/library/survival/html/
+%{_libdir}/R/library/survival/INDEX
+%{_libdir}/R/library/survival/libs/
+%{_libdir}/R/library/survival/Meta/
+%{_libdir}/R/library/survival/NAMESPACE
+%doc %{_libdir}/R/library/survival/NEWS.Rd*
+%{_libdir}/R/library/survival/R/
 # tcltk
-%{_libdir}/R/library/tcltk/
+%dir %{_libdir}/R/library/tcltk/
+%{_libdir}/R/library/tcltk/demo/
+%{_libdir}/R/library/tcltk/DESCRIPTION
+%{_libdir}/R/library/tcltk/exec/
+%{_libdir}/R/library/tcltk/help/
+%doc %{_libdir}/R/library/tcltk/html/
+%{_libdir}/R/library/tcltk/INDEX
+%{_libdir}/R/library/tcltk/libs/
+%{_libdir}/R/library/tcltk/Meta/
+%{_libdir}/R/library/tcltk/NAMESPACE
+%{_libdir}/R/library/tcltk/R/
 # tools
-%{_libdir}/R/library/tools/
+%dir %{_libdir}/R/library/tools/
+%{_libdir}/R/library/tools/DESCRIPTION
+%{_libdir}/R/library/tools/help/
+%doc %{_libdir}/R/library/tools/html/
+%{_libdir}/R/library/tools/INDEX
+%{_libdir}/R/library/tools/libs/
+%{_libdir}/R/library/tools/Meta/
+%{_libdir}/R/library/tools/NAMESPACE
+%{_libdir}/R/library/tools/R/
+%{_libdir}/R/library/tools/wre.txt
 # utils
-%{_libdir}/R/library/utils/
+%dir %{_libdir}/R/library/utils/
+%{_libdir}/R/library/utils/DESCRIPTION
+%doc %{_libdir}/R/library/utils/doc/
+%{_libdir}/R/library/utils/help/
+%doc %{_libdir}/R/library/utils/html/
+%{_libdir}/R/library/utils/iconvlist
+%{_libdir}/R/library/utils/INDEX
+%{_libdir}/R/library/utils/libs/
+%{_libdir}/R/library/utils/Meta/
+%{_libdir}/R/library/utils/misc/
+%{_libdir}/R/library/utils/NAMESPACE
+%{_libdir}/R/library/utils/R/
+%{_libdir}/R/library/utils/Sweave/
+# end of packages
 %{_libdir}/R/modules
-%{_libdir}/R/COPYING
-# %%{_libdir}/R/NEWS*
+%license %{_libdir}/R/COPYING
+# %%doc %%{_libdir}/R/NEWS*
 %{_libdir}/R/SVN-REVISION
 %{_infodir}/R-*.info*
 %{_mandir}/man1/*
 %{_pkgdocdir}
 %docdir %{_pkgdocdir}
-/etc/ld.so.conf.d/*
+%{_sysconfdir}/ld.so.conf.d/*
+%if 0%{?flatpak}
+/usr/bin/Rscript
+%endif
 
 %files core-devel
 %{_libdir}/pkgconfig/libR.pc
@@ -817,7 +951,7 @@ fi
 %endif
 
 %files -n libRmath
-%doc doc/COPYING
+%license doc/COPYING
 %{_libdir}/libRmath.so
 
 %files -n libRmath-devel
@@ -828,6 +962,104 @@ fi
 %{_libdir}/libRmath.a
 
 %changelog
+* Fri Oct 31 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.5.2-1
+- Update to 4.5.2
+
+* Tue Aug 05 2025 František Zatloukal <fzatlouk@redhat.com> - 4.5.1-3
+- Rebuilt for icu 77.1
+
+* Wed Jul 23 2025 Fedora Release Engineering <releng@fedoraproject.org> - 4.5.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
+
+* Fri Jun 13 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.5.1-1
+- Update to 4.5.1
+
+* Wed Apr 23 2025 Yaakov Selkowitz <yselkowi@redhat.com> - 4.5.0-4
+- Fix flatpak build
+
+* Fri Apr 18 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.5.0-3
+- Add libzstd-devel to Requires
+
+* Fri Apr 18 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.5.0-2
+- Add tzdata to Requires
+
+* Fri Apr 18 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.5.0-1
+- Update to 4.5.0
+
+* Fri Feb 28 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.3-1
+- Update to 4.4.3
+
+* Thu Feb 27 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.2-5
+- Remove requirement on tck/tk devel packages
+
+* Thu Jan 16 2025 Fedora Release Engineering <releng@fedoraproject.org> - 4.4.2-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
+
+* Wed Jan 15 2025 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.2-3
+- Depend on compat tcl/tk 8 for now
+- Apply upstream patch for gcc15 compatibility
+
+* Sun Dec 08 2024 Pete Walter <pwalter@fedoraproject.org> - 4.4.2-2
+- Rebuild for ICU 76
+
+* Fri Nov 01 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.2-1
+- Update to 4.4.2
+
+* Mon Jul 22 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.1-5
+- Add less back as default PAGER
+
+* Wed Jul 17 2024 Fedora Release Engineering <releng@fedoraproject.org> - 4.4.1-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
+
+* Fri Jul 05 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.1-3
+- Add libdeflate to Requires too
+
+* Thu Jul 04 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.1-2
+- Enable libdeflate
+
+* Mon Jun 17 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.1-1
+- Update to 4.4.1
+
+* Thu Apr 25 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.4.0-1
+- Update to 4.4.0
+
+* Thu Feb 29 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.3-1
+- Update to 4.3.3
+
+* Wed Jan 31 2024 Pete Walter <pwalter@fedoraproject.org> - 4.3.2-5
+- Rebuild for ICU 74
+
+* Mon Jan 22 2024 Fedora Release Engineering <releng@fedoraproject.org> - 4.3.2-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Fri Jan 19 2024 Fedora Release Engineering <releng@fedoraproject.org> - 4.3.2-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Wed Nov 01 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.2-2
+- Revert adding flexiblas to LAPACK_LIBS as per discussion with Tomas Kalibera
+
+* Tue Oct 31 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.2-1
+- Update to 4.3.2
+
+* Wed Jul 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 4.3.1-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Tue Jul 11 2023 František Zatloukal <fzatlouk@redhat.com> - 4.3.1-2
+- Rebuilt for ICU 73.2
+
+* Fri Jun 16 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.1-1
+- Update to 4.3.1
+
+* Fri Apr 21 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.0-1
+- Update to 4.3.0
+- Enable LTO (except for EPEL8)
+- Drop some tools from Requires for R-core
+- Move latex-stuff to Recommends for R-core-devel
+- Mark all html and doc folders as documentation
+
+* Thu Mar 23 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.2.3-2
+- Enable libcurl > 7
+
 * Wed Mar 15 2023 Iñaki Úcar <iucar@fedoraproject.org> - 4.2.3-1
 - Update to 4.2.3
 - Adapt license tag to SPDX

sources

@@ -1 +1 @@
-SHA512 (R-4.2.3.tar.gz) = 060bb4e1d1f1a5a0383a3b4372ac9247c0a20285020da17cebeb40ddc54da12d5f369ea243ea04d2c6970986fe22b3f9c37fbdfb3405cd8aa4f2353091ea9c5c
+SHA512 (R-4.5.2.tar.gz) = abc4ff1a1b18a1f480e7bceb3267074e30453b5a571034b4c2a1c53e1650a1bafaf86bc6ca37f117a2e4f6617039dedeedef4ba8743f38720fc70e4bed2ff0a4

update-submodules.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/bash
+
+if [ $# -eq 0 ]; then
+    >&2 echo "Usage: ./update-submodules.sh R-<version>.tar.gz"
+    exit 1
+fi
+
+TAR=$1
+DIR=$(tar tf $TAR | cut -d"/" -f1 | uniq)
+SPEC=$PWD/R.spec
+
+tar -xf $TAR
+pushd $DIR/src/library/Recommended
+for PKG in *.tar.gz; do
+    PKG="${PKG%.tar.gz}"
+    PKG_NAME="${PKG%_*}"
+    PKG_VERS="${PKG#*_}"
+    sed -i "s/submodule  $PKG_NAME.*/submodule  $PKG_NAME $PKG_VERS/" $SPEC
+    sed -i "s/R-$PKG_NAME-devel = .*/R-$PKG_NAME-devel = ${PKG_VERS//-/.}/" $SPEC
+done
+popd
+rm -rf $DIR