sagemath: update deps (on top of #58320)

common/shlibs

@@ -4190,12 +4190,12 @@ liblinbox.so.0 linbox-1.6.3_1
 libpari-gmp-tls.so.9 pari-2.17.0_1
 libtree-sitter.so.0.25 tree-sitter-0.25.2_1
 libplanarity.so.2 planarity-4.0.0.0_1
-libgap.so.9 gap-4.13.0_1
+libgap.so.10 gap-4.15.1_1
 libgtkdatabox.so.1 gtkdatabox3-1.0.0_1
 libxcvt.so.0 libxcvt-0.1.1_1
 libgf2x.so.3 gf2x-1.3.0_1
-libntl.so.44 ntl-11.5.1_1
-libflint.so.21 flintlib-3.3.1_1
+libntl.so.45 ntl-11.6.0_1
+libflint.so.22 flintlib-3.4.0_1
 libec.so.14 eclib-20241112_1
 libsymmetrica.so.3 symmetrica-3.1.0_1
 libLfunction.so.2 lcalc-2.1.0_1
@@ -4249,7 +4249,7 @@ libpolys-4.4.1.so singular-4.4.1_1
 libsingular_resources-4.4.1.so singular-4.4.1_1
 libbrial.so.3 brial-1.2.10_1
 libbrial_groebner.so.3 brial-1.2.10_1
-libm4ri.so.1 m4ri-20250128_1
+libm4ri.so.2 m4ri-20260122_1
 libm4rie.so.1 m4rie-20250128_1
 libptytty.so.0 libptytty-2.0_1
 libcoeurl.so.0.3 coeurl-0.3.0_1

srcpkgs/brial/template

@@ -1,6 +1,6 @@
 # Template file for 'brial'
 pkgname=brial
-version=1.2.14
+version=1.2.15
 revision=1
 build_style=gnu-configure
 hostmakedepends="pkg-config"
@@ -12,7 +12,7 @@ license="GPL-2.0-or-later"
 homepage="https://github.com/BRiAl/BRiAl"
 changelog="https://github.com/BRiAl/BRiAl/releases"
 distfiles="https://github.com/BRiAl/BRiAl/releases/download/$version/brial-$version.tar.bz2"
-checksum=48cd95f167381699e2c538bfbf6eac35ca046dee79f797059f3879abdf5b7e66
+checksum=1d0e7de01b1b60ad892dee6c02503f5932e2ed211f3f8dbdf1a3216c696ef201
 
 if [ -n "$CROSS_BUILD" ]; then
 	configure_args+=" --with-boost-unit-test-framework=no"

srcpkgs/eclib/template

@@ -1,7 +1,7 @@
 # Template file for 'eclib'
 pkgname=eclib
 version=20250627
-revision=3
+revision=4
 build_style=gnu-configure
 configure_args="--with-flint --with-boost --with-boost-system=c"
 makedepends="pari-devel ntl-devel flintlib-devel boost-devel-minimal

srcpkgs/flintlib/template

@@ -1,6 +1,6 @@
 # Template file for 'flintlib'
 pkgname=flintlib
-version=3.3.1
+version=3.4.0
 revision=1
 build_style=gnu-configure
 configure_args="--prefix=/usr --disable-arch $(vopt_with ntl)
@@ -14,7 +14,7 @@ license="LGPL-3.0-or-later"
 homepage="https://flintlib.org"
 changelog="https://raw.githubusercontent.com/flintlib/flint/refs/heads/main/doc/source/history.rst"
 distfiles="https://github.com/flintlib/flint/releases/download/v${version/+/-}/flint-${version/+/-}.tar.xz"
-checksum=5ee67f09ce810a0ab9f3a9de99945521b864e02064b09d6f178c60e743a8df62
+checksum=0550623c85aa37897638a6b10d267c311a788d137509692d8d858fba10a852da
 
 build_options="ntl openblas"
 desc_option_ntl="enable NTL support"

srcpkgs/gap/template

@@ -1,6 +1,6 @@
 # Template file for 'gap'
 pkgname=gap
-version=4.14.0
+version=4.15.1
 revision=1
 build_style=gnu-configure
 makedepends="gmp-devel zlib-devel readline-devel"
@@ -11,7 +11,7 @@ license="GPL-2.0-or-later"
 homepage="https://www.gap-system.org/"
 changelog="https://raw.githubusercontent.com/gap-system/gap/master/CHANGES.md"
 distfiles="https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz"
-checksum=845f5272c26feb1b8eb9ef294bf0545f264c1fe5a19b0601bbc65d79d9506487
+checksum=6049d53e99b12e25c2d848db21ac4a06380a46fe4c4157243d556fe06930042c
 
 if [ "$XBPS_CHECK_PKGS" = full ]; then
 	do_check() {

srcpkgs/m4ri/template

@@ -1,6 +1,6 @@
 # Template file for 'm4ri'
 pkgname=m4ri
-version=20250128
+version=20260122
 revision=1
 build_style=gnu-configure
 # use defaults for cache sizes instead of build machine
@@ -11,9 +11,9 @@ short_desc="Library for fast arithmetic with dense matrices over GF(2)"
 maintainer="Eloi Torrents <eloitor@duck.com>"
 license="GPL-2.0-or-later"
 homepage="https://github.com/malb/m4ri"
-changelog="https://github.com/malb/m4ri#history"
+changelog="https://github.com/malb/m4ri/releases"
 distfiles="https://github.com/malb/m4ri/releases/download/${version}/m4ri-${version}.tar.gz"
-checksum=b4098db651483c0e1506c16f79091eba02f41dadbacf1bb25be8eb97e5515f96
+checksum=7e033ca1fd36be8861e2f67d9d124c398fc0d830209bb0226462485876346404
 
 pre_check() {
 	# the testsuite is very slow when run in parallel!

srcpkgs/m4rie/template

@@ -1,15 +1,15 @@
 # Template file for 'm4rie'
 pkgname=m4rie
 version=20250128
-revision=1
+revision=2
 build_style=gnu-configure
 hostmakedepends="pkg-config"
 makedepends="m4ri-devel"
 short_desc="Library for fast arithmetic with dense matrices over GF(2^e)"
 maintainer="Eloi Torrents <eloitor@duck.com>"
 license="GPL-2.0-or-later"
 homepage="https://github.com/malb/m4rie"
-changelog="https://github.com/malb/m4rie#history"
+changelog="https://github.com/malb/m4rie/releases"
 distfiles="https://github.com/malb/m4rie/releases/download/${version}/m4rie-${version}.tar.gz"
 checksum=96f1adafd50e6a0b51dc3aa1cb56cb6c1361ae7c10d97dc35c3fa70822a55bd7
 

srcpkgs/ntl/patches/cross.patch

@@ -0,0 +1,51 @@
+--- a/src/DoConfig
++++ b/src/DoConfig
+@@ -571,7 +571,7 @@
+       # icc just gives warnings for bad command line args
+       RemoveProg("$name") and return 0;
+    }
+-   system("./$name") and RemoveProg("$name") and return 0;
++   system("\$RUNTEST ./$name") and RemoveProg("$name") and return 0;
+    RemoveProg("$name") and return 1;
+ }
+
+@@ -763,7 +763,7 @@
+    die "Goodbye!\n";
+ }
+
+-my $config_info = `./GenConfigInfo`;
++my $config_info = `\$RUNTEST ./GenConfigInfo`;
+
+ my ($compiler_name, $language_standard, $cpu_type, $os_name);
+ ($compiler_name, $language_standard, $cpu_type, $os_name) =
+--- a/src/MakeCheckFeatures
++++ b/src/MakeCheckFeatures
+@@ -14,7 +14,7 @@
+
+    if test -f CheckFeatures
+    then
+-      if ./CheckFeatures
++      if $RUNTEST ./CheckFeatures
+       then
+ 	 echo "[yes]"
+ 	 echo "#ifndef NTL_HAVE_$f" >  "../include/NTL/HAVE_$f.h"
+--- a/src/mfile
++++ b/src/mfile
+@@ -354,7 +354,7 @@
+ setup1: 
+ 	$(COMPILE) MakeDescAux.cpp
+ 	$(LINK) -o MakeDesc MakeDesc.cpp MakeDescAux.o $(LDLIBS)
+-	./MakeDesc
++	$(RUNTEST) ./MakeDesc
+ 	mv mach_desc.h ../include/NTL/mach_desc.h
+
+
+@@ -378,7 +378,7 @@
+
+ setup3:
+ 	$(LINK) $(GMP_OPT_INCDIR) -o gen_gmp_aux gen_gmp_aux.cpp $(GMP_OPT_LIBPATH) $(GMP_OPT_LIB) $(LDLIBS)
+-	./gen_gmp_aux > ../include/NTL/gmp_aux.h 
++	$(RUNTEST) ./gen_gmp_aux > ../include/NTL/gmp_aux.h 
+ 	$(LINK) $(GF2X_OPT_INCDIR) -o gf2x_version_1_2_or_later_required gf2x_version_1_2_or_later_required.cpp $(GF2X_OPT_LIBPATH) $(GF2X_OPT_LIB) $(LDLIBS) 
+
+ # setup4 runs the wizard

srcpkgs/ntl/template

@@ -1,24 +1,46 @@
 # Template file for 'ntl'
 pkgname=ntl
-version=11.5.1
+version=11.6.0
 revision=1
 build_wrksrc="src"
 build_style=configure
-hostmakedepends="perl libtool"
-makedepends="gmp-devel gf2x-devel"
+build_helper=qemu
+hostmakedepends="perl libtool autoconf automake"
+makedepends="gmp-devel gf2x-devel libtool"
 short_desc="Library for doing Number Theory"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="LGPL-2.1-or-later"
 homepage="https://libntl.org"
+changelog="https://github.com/libntl/ntl/releases"
 distfiles="https://libntl.org/ntl-${version}.tar.gz"
-checksum=210d06c31306cbc6eaf6814453c56c776d9d8e8df36d74eb306f6a523d1c6a8a
-nocross=yes # runs binaries built for target
+checksum=bc0ef9aceb075a6a0673ac8d8f47d5f8458c72fe806e4468fbd5d3daff056182
 
 build_options="native_build"
 
+if [ "$CROSS_BUILD" ]; then
+	export RUNTEST="/usr/bin/qemu-$XBPS_TARGET_QEMU_MACHINE-static"
+fi
+
+pre_configure() {
+	# project uses libtool without autoconf, which is not really viable
+	# since autoconf is supposed to configure libtool.
+	mkdir -p hack
+	cat <<-EOF >hack/configure.ac
+	AC_INIT
+	LT_INIT
+	AC_CONFIG_MACRO_DIRS([m4])
+	AC_LANG([C])
+	AC_LANG([C++])
+	LT_LANG([C])
+	LT_LANG([C++])
+	AC_OUTPUT
+	EOF
+	(cd hack;  autoreconf -fi; libtoolize -i; ./configure --host=$XBPS_CROSS_TRIPLET --build=$XBPS_TRIPLET --with-libtool-sysroot=$XBPS_CROSS_BASE)
+}
+
 do_configure() {
 	# see http://www.shoup.net/ntl/doc/tour-unix.html
-	./configure CXX="$CXX" CXXFLAGS="$CXXFLAGS" LIBTOOL="libtool" \
+	./configure CXX="$CXX" CXXFLAGS="$CXXFLAGS" LIBTOOL="./hack/libtool" \
 		PREFIX="/usr" SHARED="on" NTL_GF2X_LIB="on" \
 		NATIVE="$(vopt_if native_build 'on' 'off')"
 }
@@ -28,6 +50,7 @@ ntl-devel_package() {
 	short_desc+=" - development files"
 	pkg_install() {
 		vmove usr/include
+		vmove usr/lib/pkgconfig
 		vmove "usr/lib/*.a"
 		vmove "usr/lib/*.so"
 		vmove usr/share