sagemath: update dependencies

common/shlibs

@@ -4199,8 +4199,8 @@ libgf2x.so.3 gf2x-1.3.0_1
 libntl.so.44 ntl-11.5.1_1
 libflint.so.19 flintlib-3.1.0_1
 libec.so.14 eclib-20241112_1
-libsymmetrica.so.2 symmetrica-3.0.1_1
-libLfunction.so.1 lcalc-2.0.4_1
+libsymmetrica.so.3 symmetrica-3.1.0_1
+libLfunction.so.2 lcalc-2.1.0_1
 liblrcalc.so.2 lrcalc-2.1_1
 libwayland-client++.so.1 libwaylandpp-1.0.0_1
 libwayland-cursor++.so.1 libwaylandpp-1.0.0_1
@@ -4245,14 +4245,14 @@ libecl.so.24.5 ecl-24.5.10_1
 libecm.so.1 ecm-7.0.4_3
 libcliquer.so.1 cliquer-1.22_1
 libomalloc-0.9.6.so singular-4.2.1_1
-libSingular-4.4.0.so singular-4.4.0_1
-libfactory-4.4.0.so singular-4.4.0_1
-libpolys-4.4.0.so singular-4.4.0_1
-libsingular_resources-4.4.0.so singular-4.4.0_1
+libSingular-4.4.1.so singular-4.4.1_1
+libfactory-4.4.1.so singular-4.4.1_1
+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-0.0.20200125.so m4ri-20200125_1
-libm4rie-0.0.20200125.so m4rie-20200125_1
+libm4ri.so.1 m4ri-20250128_1
+libm4rie.so.1 m4rie-20250128_1
 libptytty.so.0 libptytty-2.0_1
 libcoeurl.so.0.3 coeurl-0.3.0_1
 libKPim6PkPass.so.6 kpkpass-24.02.0_1

srcpkgs/brial/template

@@ -1,7 +1,7 @@
 # Template file for 'brial'
 pkgname=brial
 version=1.2.12
-revision=1
+revision=2
 build_style=gnu-configure
 hostmakedepends="pkg-config"
 makedepends="boost-devel m4ri-devel"

srcpkgs/eclib/template

@@ -1,6 +1,6 @@
 # Template file for 'eclib'
 pkgname=eclib
-version=20241112
+version=20250122
 revision=1
 build_style=gnu-configure
 configure_args="--with-flint --with-boost"
@@ -10,8 +10,8 @@ maintainer="Gonzalo Tornaría <[email protected]>"
 license="GPL-2.0-or-later"
 homepage="https://github.com/JohnCremona/eclib"
 changelog="https://github.com/JohnCremona/eclib/releases"
-distfiles="https://github.com/JohnCremona/eclib/releases/download/v${version}/eclib-${version}.tar.bz2"
-checksum=30765c27ca1420141f83517897119d0185fea9b31132392170ddae40b060e46f
+distfiles="https://github.com/JohnCremona/eclib/releases/download/${version}/eclib-${version}.tar.bz2"
+checksum=9f8c2b32e24a4f20d7cc2d336ea30c8ea03b5b0953c2d32adda0c496e7616899
 
 eclib-devel_package() {
 	depends="${sourcepkg}>=${version}_${revision} ntl-devel"

srcpkgs/flintlib/template

@@ -1,19 +1,19 @@
 # Template file for 'flintlib'
 pkgname=flintlib
-version=3.1.2
-revision=2
+version=3.1.3+p1
+revision=1
 build_style=gnu-configure
 configure_args="--prefix=/usr --disable-arch $(vopt_with ntl)
  $(vopt_if openblas --with-blas-include=${XBPS_CROSS_BASE}/usr/include/openblas)"
 makedepends="mpfr-devel $(vopt_if ntl ntl-devel)
  $(vopt_if openblas openblas-devel)"
 short_desc="Fast Library for Number Theory"
 maintainer="Gonzalo Tornaría <[email protected]>"
-license="LGPL-2.1-or-later"
+license="LGPL-3.0-or-later"
 homepage="https://flintlib.org"
-changelog="https://raw.githubusercontent.com/wbhart/flint2/trunk/NEWS"
-distfiles="https://flintlib.org/flint-${version}.tar.gz"
-checksum=fdb3a431a37464834acff3bdc145f4fe8d0f951dd5327c4c6f93f4cbac5c2700
+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=8d75df8f2347534bd3245ef6f43cb91e43abd152572c6fe0bfffda55ec014920
 
 build_options="ntl openblas"
 desc_option_ntl="enable NTL support"

srcpkgs/flintlib/update

@@ -1,3 +1,5 @@
-# package was named 'flintlib' because of another package
-pkgname=flint
-site="https://flintlib.org/downloads.html"
+pattern="/archive/refs/tags/v?\K[\d.]+(-(p|rc)[0-9]+)?(?=\.tar\.gz)"
+version=${version/+/.}
+if [[ "$version" != *rc* ]]; then
+	ignore=*rc*
+fi

srcpkgs/lcalc/template

@@ -1,7 +1,7 @@
 # Template file for 'lcalc'
 pkgname=lcalc
-version=2.0.5
-revision=3
+version=2.1.0
+revision=1
 build_style=gnu-configure
 configure_args="--with-pari"
 hostmakedepends="automake libtool pkg-config gengetopt"
@@ -12,7 +12,12 @@ license="GPL-2.0-or-later"
 homepage="https://gitlab.com/sagemath/lcalc"
 changelog="https://gitlab.com/sagemath/lcalc/-/raw/master/doc/ChangeLog"
 distfiles="https://gitlab.com/sagemath/lcalc/-/archive/${version}/lcalc-${version}.tar.bz2"
-checksum=94efc160a2761de75df534707fd2ec53949c5389296d20ddbac1b285fe26d1ad
+checksum=463f26cc42262a90440fcec95a56cc267f00d6ac9870dfe1f4838359696664d5
+
+case $XBPS_TARGET_MACHINE in
+	# avoid numerical noise caused by extended-precision of registers
+	i686*) CXXFLAGS="-mfpmath=sse -msse2" ;;
+esac
 
 pre_configure() {
 	autoreconf -fi

srcpkgs/m4ri/patches/fix-overflow-32bit.patch

@@ -0,0 +1,35 @@
+diff --git a/m4ri/mmc.h b/m4ri/mmc.h
+index e6db4ca..3e97391 100644
+--- a/m4ri/mmc.h
++++ b/m4ri/mmc.h
+@@ -72,6 +72,10 @@ typedef struct _mm_block {
+  * \return Pointer to allocated memory block.
+  */
+ static inline void *m4ri_mmc_calloc(size_t count, size_t size) {
++  if (size && count > SIZE_MAX/size) {
++      m4ri_die("m4ri_mmc_calloc: overflow in multiplication\n");
++      return NULL; /* unreachable */
++  }
+   size_t total_size = count * size;
+   void *ret         = m4ri_mmc_malloc(total_size);
+   memset((char *)ret, 0, total_size);
+diff --git a/m4ri/mzd.c b/m4ri/mzd.c
+index ba04b7c..ac62c5c 100644
+--- a/m4ri/mzd.c
++++ b/m4ri/mzd.c
+@@ -144,13 +144,12 @@ mzd_t *mzd_init(rci_t r, rci_t c) {
+   mzd_t *A = mzd_t_malloc();
+   A->nrows         = r;
+   A->ncols         = c;
+-  A->width         = (c + m4ri_radix - 1) / m4ri_radix;
++  A->width         = c > 0 ? (c - 1) / m4ri_radix + 1 : 0;
+   A->rowstride     = ((A->width & 1) == 0) ? A->width : A->width + 1;
+   A->high_bitmask  = __M4RI_LEFT_BITMASK(c % m4ri_radix);
+   A->flags         = (A->high_bitmask != m4ri_ffff) ? mzd_flag_nonzero_excess : 0;
+   if (r && c) {
+-    size_t block_words = r * A->rowstride;
+-    A->data = m4ri_mmc_calloc(block_words, sizeof(word));
++    A->data = m4ri_mmc_calloc(r, sizeof(word) * A->rowstride);
+   } else {
+     A->data = NULL;
+   }

srcpkgs/m4ri/template

@@ -1,17 +1,24 @@
 # Template file for 'm4ri'
 pkgname=m4ri
-version=20200125
-revision=2
+version=20250128
+revision=1
 build_style=gnu-configure
-configure_args="--enable-openmp ax_cv_have_sse3_ext=no ax_cv_have_ssse3_ext=no"
+# use defaults for cache sizes instead of build machine
+configure_args="--enable-openmp --with-cachesize=0:0:0"
 hostmakedepends="pkg-config"
 makedepends="libgomp-devel libpng-devel"
 short_desc="Library for fast arithmetic with dense matrices over GF(2)"
-maintainer="Eloi Torrents <eloitorrentsj@gmail.com>"
+maintainer="Eloi Torrents <eloitor@duck.com>"
 license="GPL-2.0-or-later"
-homepage="https://bitbucket.org/malb/m4ri"
-distfiles="https://bitbucket.org/malb/m4ri/downloads/${pkgname}-${version}.tar.gz"
-checksum=0dfb34aed351882a0f2281535ea6f81c690a5efeb14edab131d9ba0dffe44863
+homepage="https://github.com/malb/m4ri"
+changelog="https://github.com/malb/m4ri#history"
+distfiles="https://github.com/malb/m4ri/releases/download/${version}/m4ri-${version}.tar.gz"
+checksum=b4098db651483c0e1506c16f79091eba02f41dadbacf1bb25be8eb97e5515f96
+
+pre_check() {
+	# the testsuite is very slow when run in parallel!
+	unset makejobs
+}
 
 m4ri-devel_package() {
 	short_desc+=" - development files"

srcpkgs/m4rie/template

@@ -1,19 +1,26 @@
 # Template file for 'm4rie'
 pkgname=m4rie
-version=20200125
-revision=2
+version=20250128
+revision=1
 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 <eloi.torrentsj@gmail.com>"
+maintainer="Eloi Torrents <eloitor@duck.com>"
 license="GPL-2.0-or-later"
-homepage="https://bitbucket.org/malb/m4rie/wiki/Home"
-distfiles="https://bitbucket.org/malb/m4rie/downloads/m4rie-${version}.tar.gz"
-checksum=7f3107f7cd10f6c22d9663d9536e1af2f551e10183601852a60d760918caf58d
+homepage="https://github.com/malb/m4rie"
+changelog="https://github.com/malb/m4rie#history"
+distfiles="https://github.com/malb/m4rie/releases/download/${version}/m4rie-${version}.tar.gz"
+checksum=96f1adafd50e6a0b51dc3aa1cb56cb6c1361ae7c10d97dc35c3fa70822a55bd7
+
+pre_check() {
+	# the testsuite is very slow when run in parallel!
+	unset makejobs
+}
 
 m4rie-devel_package() {
 	short_desc+=" - development files"
-	depends="${sourcepkg}>=${version}_${revision}"
+	depends="${sourcepkg}>=${version}_${revision} ${makedepends}"
 	pkg_install() {
 		vmove usr/include
 		vmove "usr/lib/*.a"

srcpkgs/python3-cysignals/template

@@ -1,6 +1,6 @@
 # Template file for 'python3-cysignals'
 pkgname=python3-cysignals
-version=1.12.2
+version=1.12.3
 revision=1
 build_style=python3-pep517
 build_helper=meson
@@ -14,7 +14,7 @@ license="LGPL-3.0-or-later"
 homepage="https://github.com/sagemath/cysignals"
 changelog="https://github.com/sagemath/cysignals/releases"
 distfiles="${PYPI_SITE}/c/cysignals/cysignals-${version}.tar.gz"
-checksum=407db178fb18a91118ca742ede62000b2bee62b617eb49d26fcdad7e9ba2771a
+checksum=89f7626dbf29db5ab3d6eff15a89978f4eb5193c320e9099bcc157dacdefd1eb
 
 # cysignals must be compiled without _FORTIFY_SOURCE
 CFLAGS="-U_FORTIFY_SOURCE"