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

@@ -54,3 +54,10 @@
 /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-CVE-2024-27322.patch

@@ -1,49 +0,0 @@
-From f7c46500f455eb4edfc3656c3fa20af61b16abb7 Mon Sep 17 00:00:00 2001
-From: luke <luke@00db46b3-68df-0310-9c12-caf00c1e9a41>
-Date: Sun, 31 Mar 2024 19:35:58 +0000
-Subject: [PATCH] readRDS() and unserialize() now signal an errorr instead of
- returning a PROMSXP.
-
-git-svn-id: https://svn.r-project.org/R/trunk@86235 00db46b3-68df-0310-9c12-caf00c1e9a41
----
- src/main/serialize.c | 13 ++++++++++---
- 1 file changed, 10 insertions(+), 3 deletions(-)
-
-diff --git a/src/main/serialize.c b/src/main/serialize.c
-index a389f713116..a190fbf8f3c 100644
---- a/src/main/serialize.c
-+++ b/src/main/serialize.c
-@@ -2650,6 +2650,13 @@ do_serializeToConn(SEXP call, SEXP op, SEXP args, SEXP env)
-     return R_NilValue;
- }
- 
-+static SEXP checkNotPromise(SEXP val)
-+{
-+    if (TYPEOF(val) == PROMSXP)
-+	error(_("cannot return a promise (PROMSXP) object"));
-+    return val;
-+}
-+
- /* unserializeFromConn(conn, hook) used from readRDS().
-    It became public in R 2.13.0, and that version added support for
-    connections internally */
-@@ -2699,7 +2706,7 @@ do_unserializeFromConn(SEXP call, SEXP op, SEXP args, SEXP env)
- 	con->close(con);
- 	UNPROTECT(1);
-     }
--    return ans;
-+    return checkNotPromise(ans);
- }
- 
- /*
-@@ -3330,8 +3337,8 @@ attribute_hidden SEXP
- do_serialize(SEXP call, SEXP op, SEXP args, SEXP env)
- {
-     checkArity(op, args);
--    if (PRIMVAL(op) == 2) return R_unserialize(CAR(args), CADR(args));
--
-+    if (PRIMVAL(op) == 2) //return R_unserialize(CAR(args), CADR(args));
-+	return checkNotPromise(R_unserialize(CAR(args), CADR(args)));
-     SEXP object, icon, type, ver, fun;
-     object = CAR(args); args = CDR(args);
-     icon = CAR(args); args = CDR(args);

R.spec

@@ -27,15 +27,15 @@
 
 # Should be the previous version, to make mass-rebuilds easier
 %bcond_with bootstrap
-%global bootstrap_abi 4.2
+%global bootstrap_abi 4.4
 
 %global major_version 4
-%global minor_version 3
-%global patch_version 3
+%global minor_version 5
+%global patch_version 2
 
 Name:           R
 Version:        %{major_version}.%{minor_version}.%{patch_version}
-Release:        2%{?dist}
+Release:        1%{?dist}
 Summary:        A language for data analysis and graphics
 
 License:        GPL-2.0-or-later
@@ -43,9 +43,6 @@ URL:            https://www.r-project.org
 Source0:        https://cran.r-project.org/src/base/R-4/R-%{version}.tar.gz
 # see https://bugzilla.redhat.com/show_bug.cgi?id=1324145
 Patch0:         R-3.3.0-fix-java_path-in-javareconf.patch
-# see https://bugzilla.redhat.com/show_bug.cgi?id=2277884
-# https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7
-Patch1:         R-CVE-2024-27322.patch
 
 BuildRequires:  gcc-gfortran
 BuildRequires:  gcc-c++
@@ -63,6 +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
@@ -81,6 +80,7 @@ BuildRequires:  java-devel
 BuildRequires:  autoconf
 BuildRequires:  automake
 BuildRequires:  libtool
+BuildRequires:  less
 BuildRequires:  tex(latex)
 BuildRequires:  texinfo-tex
 BuildRequires:  tex(upquote.sty)
@@ -112,6 +112,8 @@ and called at run time.
 %package core
 Summary:        The minimal R components necessary for a functional runtime
 Requires:       libRmath%{?_isa} = %{version}-%{release}
+Requires:       tzdata
+Requires:       less
 Requires:       xdg-utils
 Requires:       zip, unzip
 
@@ -138,32 +140,32 @@ Provides:       R(ABI) = %{bootstrap_abi}
   print("Provides: R(" .. name .. ") = " .. rpm_version)
 }
 %add_submodule  base %{version}
-%add_submodule  boot 1.3-29
-%add_submodule  class 7.3-22
-%add_submodule  cluster 2.1.6
-%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 0.8-86
+%add_submodule  foreign 0.8-90
 %add_submodule  graphics %{version}
 %add_submodule  grDevices %{version}
 %add_submodule  grid %{version}
-%add_submodule  KernSmooth 2.23-22
-%add_submodule  lattice 0.22-5
-%add_submodule  MASS 7.3-60.0.1
-%add_submodule  Matrix 1.6-5
+%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 1.9-1
-%add_submodule  nlme 3.1-164
-%add_submodule  nnet 7.3-19
+%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 4.1.23
-%add_submodule  spatial 7.3-17
+%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 3.5-8
+%add_submodule  survival 3.8-3
 %add_submodule  tcltk %{version}
 %add_submodule  tools %{version}
 %add_submodule  translations %{version}
@@ -194,12 +196,12 @@ 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
@@ -217,7 +219,7 @@ Recommends:     tex(inconsolata.sty)
 Recommends:     qpdf
 %endif
 
-Provides:       R-Matrix-devel = 1.6.5
+Provides:       R-Matrix-devel = 1.7.4
 Obsoletes:      R-Matrix-devel < 0.999375-7
 
 %ifarch %{java_arches}
@@ -306,12 +308,15 @@ from the R project.  This package provides the static libRmath library.
 %prep
 %setup -q
 %patch -P0 -p1 -b .fixpath
-%patch -P1 -p1 -b .fixcve
+# 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"
@@ -331,8 +336,8 @@ export JAVA_HOME=%{_jvmdir}/jre
   --with-system-tre \
   --with-blas=%{blaslib}%{blasvar} \
   --with-lapack \
-  --with-tcl-config=%{_libdir}/tclConfig.sh \
-  --with-tk-config=%{_libdir}/tkConfig.sh \
+  --with-tcl-config=/usr/%{_lib}/tclConfig.sh \
+  --with-tk-config=/usr/%{_lib}/tkConfig.sh \
   --enable-R-shlib \
   --enable-prebuilt-html \
   --enable-R-profiling \
@@ -399,6 +404,12 @@ for i in tex/latex bibtex/bib bibtex/bst; do
   (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}
 # Needed by tests/ok-error.R, which will smash the stack on PPC64.
@@ -438,21 +449,30 @@ TZ="Europe/Paris" make check
 %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
 %dir %{_libdir}/R/library/base/
@@ -691,6 +711,7 @@ TZ="Europe/Paris" make check
 %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
@@ -883,6 +904,7 @@ TZ="Europe/Paris" make check
 %{_libdir}/R/library/tools/Meta/
 %{_libdir}/R/library/tools/NAMESPACE
 %{_libdir}/R/library/tools/R/
+%{_libdir}/R/library/tools/wre.txt
 # utils
 %dir %{_libdir}/R/library/utils/
 %{_libdir}/R/library/utils/DESCRIPTION
@@ -907,6 +929,9 @@ TZ="Europe/Paris" make check
 %{_pkgdocdir}
 %docdir %{_pkgdocdir}
 %{_sysconfdir}/ld.so.conf.d/*
+%if 0%{?flatpak}
+/usr/bin/Rscript
+%endif
 
 %files core-devel
 %{_libdir}/pkgconfig/libR.pc
@@ -937,8 +962,66 @@ TZ="Europe/Paris" make check
 %{_libdir}/libRmath.a
 
 %changelog
-* Tue Apr 30 2024 Iñaki Úcar <iucar@fedoraproject.org> - 4.3.3-2
-- Security fix for CVE-2024-27322
+* 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

sources

@@ -1 +1 @@
-SHA512 (R-4.3.3.tar.gz) = 26291590d935ea5678771cdcaea013a6c030897eb762b0204e42b34b0f1d33aac1ec933f36caa18d2a31a057a4456bf629222e4f5679f24bc48a7a764b1aedbe
+SHA512 (R-4.5.2.tar.gz) = abc4ff1a1b18a1f480e7bceb3267074e30453b5a571034b4c2a1c53e1650a1bafaf86bc6ca37f117a2e4f6617039dedeedef4ba8743f38720fc70e4bed2ff0a4