void-linux · tornaria · Oct 11, 2022 · Oct 11, 2022 · Oct 10, 2022 · Oct 10, 2022
diff --git a/common/shlibs b/common/shlibs
@@ -4011,18 +4011,17 @@ libsimavrparts.so.1 simavr-1.6_2
 libsword-1.8.1.so libsword-1.8.1_6
 libgivaro.so.9 givaro-4.1.1_1
 liblinbox.so.0 linbox-1.6.3_1
-libpari-gmp.so.7 pari-2.13.0_1
-libpari-gmp-tls.so.7 pari-2.13.2_1
+libpari-gmp-tls.so.8 pari-2.15.0_1
 libtree-sitter.so.0 tree-sitter-0.19.0_1
 libplanarity.so.0 planarity-3.0.1.1_1
-libgap.so.0 gap-4.11.1_1
+libgap.so.8 gap-4.12.0_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.16 flintlib-2.8.0_1
+libflint.so.17 flintlib-2.9.0_1
 libarb.so.2 arb-2.20.0_1
-libec.so.8 eclib-20210625_1
+libec.so.10 eclib-20220621_1
 libsymmetrica.so.2 symmetrica-3.0.1_1
 libLfunction.so.1 lcalc-2.0.4_1
 liblrcalc.so.2 lrcalc-2.1_1
@@ -4062,11 +4061,11 @@ libumfpack.so.5 SuiteSparse-5.10.1_1
 libecl.so.21.2 ecl-21.2.1_1
 libecm.so.1 ecm-7.0.4_3
 libcliquer.so.1 cliquer-1.22_1
-libSingular-4.3.0.so singular-4.3.0_1
-libfactory-4.3.0.so singular-4.3.0_1
-libpolys-4.3.0.so singular-4.3.0_1
-libomalloc-0.9.6.so singular-4.3.0_1
-libsingular_resources-4.3.0.so singular-4.3.0_1
+libSingular-4.3.1.so singular-4.3.1p2_1
+libfactory-4.3.1.so singular-4.3.1p2_1
+libpolys-4.3.1.so singular-4.3.1p2_1
+libomalloc-0.9.6.so singular-4.3.1p2_1
+libsingular_resources-4.3.1.so singular-4.3.1p2_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

diff --git a/srcpkgs/arb/template b/srcpkgs/arb/template
@@ -1,6 +1,6 @@
 # Template file for 'arb'
 pkgname=arb
-version=2.22.1
+version=2.23.0
 revision=1
 build_style=configure
 configure_args="--prefix=/usr --with-gmp=/usr --with-mpfr=/usr --with-flint=/usr"
@@ -11,9 +11,7 @@ license="LGPL-2.1-or-later"
 homepage="https://arblib.org"
 changelog="https://raw.githubusercontent.com/fredrik-johansson/arb/master/doc/source/history.rst"
 distfiles="https://github.com/fredrik-johansson/arb/archive/${version}.tar.gz"
-checksum=1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243
-
-CFLAGS="-D_GNU_SOURCE" # needed for cpu_set_t
+checksum=977d41bde46f5442511d5165c705cec32c03e852c84d7d1836135d412ce702bb
 
 arb-devel_package() {
 	depends="${sourcepkg}>=${version}_${revision} ${makedepends}"

diff --git a/srcpkgs/eclib/template b/srcpkgs/eclib/template
@@ -1,7 +1,7 @@
 # Template file for 'eclib'
 pkgname=eclib
-version=20210625
-revision=2
+version=20221012
+revision=1
 build_style=gnu-configure
 configure_args="--with-flint --with-boost"
 hostmakedepends="automake autoconf-archive libtool"
@@ -11,7 +11,7 @@ maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://github.com/JohnCremona/eclib"
 distfiles="https://github.com/JohnCremona/eclib/archive/refs/tags/${version}.tar.gz"
-checksum=00333fd36afd237c9e6e410c7ab98536ddcd7fdc430e6837fe293247b835c572
+checksum=bd6f0191876c1426ca57db851ce06ef79ea1755f01e81dd747358d1b76b5e932
 
 pre_configure() {
 	autoreconf -fi

diff --git a/srcpkgs/flintlib/template b/srcpkgs/flintlib/template
@@ -1,6 +1,6 @@
 # Template file for 'flintlib'
 pkgname=flintlib
-version=2.8.5
+version=2.9.0
 revision=1
 wrksrc="flint-${version}"
 build_style=configure
@@ -14,11 +14,10 @@ license="LGPL-2.1-or-later"
 homepage="https://flintlib.org"
 changelog="https://raw.githubusercontent.com/wbhart/flint2/trunk/NEWS"
 distfiles="https://flintlib.org/flint-${version}.tar.gz"
-checksum=5911fedff911100f15781f35e3a4fa934fe60e4aea02a8c10cc8918101c1eed8
+checksum=2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a
 
 build_options="ntl openblas"
 desc_option_ntl="enable NTL support"
-build_options_default=""
 
 if [ -z "$CROSS_BUILD" ]; then
 	build_options_default+=" ntl"

diff --git a/srcpkgs/gap/patches/atlasrep-dont_use_network_by_default.patch b/srcpkgs/gap/patches/atlasrep-dont_use_network_by_default.patch
@@ -0,0 +1,11 @@
+--- a/pkg/atlasrep/gap/userpref.g	2022-09-06 17:41:17.000000000 -0300
++++ b/pkg/atlasrep/gap/userpref.g	2022-10-29 07:46:48.580833277 -0300
+@@ -46,7 +46,7 @@
+ this information depends on the value of the preference at the time \
+ when the AtlasRep package and its data extensions get loaded."
+     ],
+-  default:= true,
++  default:= false,
+   values:= [ true, false ],
+   multi:= false,
+   package:= "AtlasRep",
diff --git a/srcpkgs/gap/template b/srcpkgs/gap/template
@@ -1,17 +1,17 @@
 # Template file for 'gap'
 pkgname=gap
-version=4.11.1
+version=4.12.1
 revision=1
 build_style=gnu-configure
-make_install_target="install-bin install-gaproot install-headers install-libgap"
 makedepends="gmp-devel zlib-devel readline-devel"
 checkdepends="perl"
 short_desc="Groups, Algorithms, Programming - computational discrete algebra"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
-homepage="http://www.gap-system.org/"
+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=6635c5da7d82755f8339486b9cac33766f58712f297e8234fba40818902ea304
+checksum=f9ebef11ee31b210ce36e3c70960742b4e253282bbd5270adc9324273c92b016
 
 if [ "$XBPS_CHECK_PKGS" = full ]; then
 	# not sure about this -- takes about 25 minutes
@@ -21,20 +21,36 @@ fi
 _GAPROOT=/usr/share/gap/
 
 # minimal required packages
-_GAPPKGS="GAPDoc primgrp SmallGrp transgrp"
+_GAPPKGS="autodoc gapdoc primgrp smallgrp transgrp"
 
 # other expected packages
-_GAPPKGS+=" atlasrep autpgrp alnuth crisp ctbllib FactInt fga irredsol laguna
- polenta polycyclic resclasses sophus tomlib"
+_GAPPKGS+=" atlasrep autpgrp alnuth crisp ctbllib factint fga irredsol laguna
+ polenta polycyclic radiroot resclasses sophus tomlib utils"
 
-post_install() {
-	vmkdir ${_GAPROOT}/pkg
+post_extract() {
+	# keep around only the packages that we want to install
+	mkdir pkg.install
 	for p in ${_GAPPKGS}; do
-		[ -d pkg/$p ] || p="$p-*"
-		vcopy "pkg/$p" ${_GAPROOT}/pkg
+		mv "pkg/$p" pkg.install
 	done
-	# not handled by make install-headers
-	vcopy gen/config.h /usr/include/gap
+	mv pkg pkg.orig
+	mv pkg.install pkg
+}
+
+post_install() {
+	vmkdir ${_GAPROOT}
+	vcopy pkg ${_GAPROOT}
+}
+
+pre_check() {
+	msg_normal "Check that loading packages works\n"
+	for p in ${_GAPPKGS}; do
+		cat <<-EOF
+		if LoadPackage("$p") <> true then
+		    Error("loading package '$p'");
+		fi;
+		EOF
+	done | ./gap --quitonbreak -b -q -r
 }
 
 gap-devel_package() {

diff --git a/srcpkgs/giac/patches/giac-pari-2.15-test.patch b/srcpkgs/giac/patches/giac-pari-2.15-test.patch
@@ -0,0 +1,10 @@
+Fix a failing test due to thread stack overflow
+
+--- a/check/chk_fhan4	2018-03-13 15:27:11.000000000 -0300
++++ b/check/chk_fhan4	2022-10-14 18:51:12.604731890 -0300
+@@ -1,4 +1,5 @@
+ #! /bin/sh
+ unset LANG
++export PARI_SIZE=2048000
+ ../src/icas TP04-sol.cas > TP04.tst
+ diff TP04.tst TP04-sol.cas.out1
diff --git a/srcpkgs/giac/patches/giac-pari-2.15.patch b/srcpkgs/giac/patches/giac-pari-2.15.patch
@@ -0,0 +1,20 @@
+ANYARG patch
+
+diff --git a/src/pari.cc b/src/pari.cc
+index 76ce8e1..50d08ab 100644
+--- a/src/pari.cc
++++ b/src/pari.cc
+@@ -40,6 +40,13 @@ using namespace std;
+
+ #ifdef HAVE_LIBPARI
+
++// Anyarg disappeared from PARI 2.15.0
++#ifdef __cplusplus
++#  define ANYARG ...
++#else
++#  define ANYARG
++#endif
++
+ #ifdef HAVE_PTHREAD_H
+ #include <pthread.h>
+ #endif
diff --git a/srcpkgs/giac/template b/srcpkgs/giac/template
@@ -1,6 +1,6 @@
 # Template file for 'giac'
 pkgname=giac
-version=1.9.0.7
+version=1.9.0.27
 revision=1
 wrksrc="giac-${version%.*}"
 build_style=gnu-configure
@@ -14,7 +14,7 @@ license="GPL-3.0-or-later"
 homepage="https://www-fourier.ujf-grenoble.fr/~parisse/giac.html"
 changelog="https://www-fourier.ujf-grenoble.fr/~parisse/install_en#new"
 distfiles="https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version%.*}-${version##*.}.tar.gz"
-checksum=72016988b7180e9b630ecabecc60969213e7b61418c2598c91acbaec139fd740
+checksum=c5d222fbff5db2a0a560b4e106ce88dd13d109ecb21570a939b8b3b87521d5e0
 
 # need more than 4*65536 stack, see try_parse() in gen.cc line 11812
 LDFLAGS="-Wl,-z,stack-size=2097152"

diff --git a/srcpkgs/gp2c/template b/srcpkgs/gp2c/template
@@ -1,6 +1,6 @@
 # Template file for 'gp2c'
 pkgname=gp2c
-version=0.0.12pl1
+version=0.0.13
 revision=1
 build_style=gnu-configure
 hostmakedepends="perl"
@@ -12,4 +12,4 @@ license="GPL-2.0-or-later"
 homepage="http://pari.math.u-bordeaux.fr/"
 changelog="http://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=gp2c.git;a=blob_plain;f=ChangeLog;hb=HEAD"
 distfiles="${homepage}pub/pari/GP2C/${pkgname}-${version}.tar.gz"
-checksum=79a8c46f7ad3331e4d8ae6af6b496c4742fd73a73b996b3ca7ead61452ca6e8d
+checksum=261374eca73ebd76c112a9593dca28b64812aa762561fda5a4b2c2cd79a69d36
diff --git a/srcpkgs/lcalc/template b/srcpkgs/lcalc/template
@@ -1,7 +1,7 @@
 # Template file for 'lcalc'
 pkgname=lcalc
 version=2.0.5
-revision=1
+revision=2
 build_style=gnu-configure
 configure_args="--with-pari"
 hostmakedepends="automake libtool pkg-config gengetopt"

diff --git a/srcpkgs/pari/patches/9c4bcd3f497f30f757c8eecadc9b45b33754a540.patch b/srcpkgs/pari/patches/9c4bcd3f497f30f757c8eecadc9b45b33754a540.patch
@@ -0,0 +1,54 @@
+See: https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2419
+--
+
+commit 9c4bcd3f497f30f757c8eecadc9b45b33754a540
+Author: Karim Belabas <Karim.Belabas@math.u-bordeaux.fr>
+Date:   Tue Oct 4 10:30:43 2022 +0200
+
+    6- conversion to float of t_QUAD with t_FRAC components [#2419]
+
+diff --git a/src/basemath/gen2.c b/src/basemath/gen2.c
+index 3ef74a7023..d810270b99 100644
+--- a/src/basemath/gen2.c
++++ b/src/basemath/gen2.c
+@@ -2429,8 +2429,8 @@ quadtofp(GEN x, long prec)
+   else
+   { /* if (b) x ~ (u + z) / 2 and quadnorm(x) ~ (u^2 - z^2) / 4
+      * else x ~ u + z and quadnorm(x) ~ u^2 - z^2 */
+-    long s = signe(u);
+-    if (s == -signe(v)) /* conjugate expression avoids cancellation */
++    long s = gsigne(u);
++    if (s == -gsigne(v)) /* conjugate expression avoids cancellation */
+     {
+       z = gdiv(quadnorm(x), gsub(u, z));
+       if (b) shiftr_inplace(z, 1);
+diff --git a/src/test/32/quad b/src/test/32/quad
+index 2b43d87a4a..1f1042d143 100644
+--- a/src/test/32/quad
++++ b/src/test/32/quad
+@@ -43,6 +43,7 @@ w
+ -4294967297
+ 4294967297
+ -4294967297
++2.2847006554165615148712535010323047844
+   ***   at top-level: floor(w8)
+   ***                 ^---------
+   *** floor: incorrect type in gfloor (t_QUAD).
+@@ -55,4 +56,4 @@ w
+   ***   at top-level: floor(Mod(0,3)*quadgen(5))
+   ***                 ^--------------------------
+   *** floor: incorrect type in gfloor (t_QUAD).
+-Total time spent: 2
++Total time spent: 1
+diff --git a/src/test/in/quad b/src/test/in/quad
+index c8cd5a586f..82cd5e992d 100644
+--- a/src/test/in/quad
++++ b/src/test/in/quad
+@@ -47,6 +47,7 @@ ceil(2*w)
+ ceil(-2*w)
+ round(2*w)
+ round(-2*w)
++quadgen(5) + 2/3 + 0.\\ #2419
+
+ \\ Errors keep at end of file
+ floor(w8)
diff --git a/srcpkgs/pari/patches/float32.patch b/srcpkgs/pari/patches/float32.patch
@@ -0,0 +1,48 @@
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Fri Oct 14 17:00:46 2022 -0300
+
+    Revert "x86 (32bit): force -mpc64 on compilers that supports it."
+
+    This reverts commit ca61b6391cf95ac8af15669236e2ec5839d2ad91.
+
+
+This causes problems with floating point precision on i686:
+```
+$ cat exp40.c
+#include <math.h>
+#include <stdio.h>
+int main() {
+	volatile int a=40; /* do not optimize away the call to exp(a) */
+	printf("%f\n", exp(a));
+}
+$ cc -Wall exp40.c -lm && ./a.out
+235385266837020000.000000
+$ cc -Wall exp40.c -lm -mpc64 && ./a.out
+235385266837020448.000000
+```
+
+Note that when pari is built using -mpc64, just *linking* with -lpari
+causes the problem!!!
+```
+$ cc -Wall exp40.c -lm -lpari && ./a.out
+235385266837020448.000000
+```
+
+diff --git a/config/get_cc b/config/get_cc
+index 3cfaa88bb7..2d61d3871f 100644
+--- a/config/get_cc
++++ b/config/get_cc
+@@ -110,13 +110,6 @@ if test -n "$__gnuc__"; then
+   # Specific optimisations for some architectures
+   case "$arch" in
+     sparcv8*) cflags=-mv8;;
+-    i?86)
+-      cmd="$CC $CFLAGS $extraflag -mpc64 -fno-strict-aliasing -o $exe gnu.c"
+-      . log_cmd
+-      if test -s $exe; then
+-        cflags="-mpc64"
+-      fi
+-      . cleanup_exe;;
+   esac
+   # problems on some architectures
+   case "$osname" in
diff --git a/srcpkgs/pari/template b/srcpkgs/pari/template
@@ -1,6 +1,6 @@
 # Template file for 'pari'
 pkgname=pari
-version=2.13.4
+version=2.15.0
 revision=1
 build_style=configure
 build_helper=qemu
@@ -11,14 +11,15 @@ make_check_target=statest-all
 make_install_target="install install-lib-sta install-lib-dyn"
 hostmakedepends="perl texlive"
 makedepends="gmp-devel readline-devel $(vopt_if x11 libX11-devel)"
-checkdepends="pari-elldata-small pari-galdata pari-galpol-small pari-seadata-small"
+checkdepends="pari-elldata-small pari-galdata pari-galpol-small
+ pari-seadata-small pari-nflistdata"
 short_desc="Fast computations library in number theory"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://pari.math.u-bordeaux.fr"
 changelog="https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=blob_plain;f=CHANGES;hb=refs/heads/pari-${version%.*}"
 distfiles="https://pari.math.u-bordeaux.fr/pub/pari/unix/${pkgname}-${version}.tar.gz"
-checksum=bcde9eceae1592814381c1697cdb7063567b6504201b1be47bb58920f3bce185
+checksum=e474851e0d16d4e4f9a0d9612c746a2ae7c9a1ec185d04c440b1c74a85755685
 
 build_options="x11 pthreads"
 build_options_default="x11 pthreads"
@@ -27,6 +28,11 @@ desc_option_pthreads="Enable support for pthreads"
 # reduce speed losses due to pthreads
 CFLAGS="-flto -fno-semantic-interposition"
 
+case $XBPS_TARGET_MACHINE in
+	# avoid numerical noise caused by extended-precision of registers
+	i686*) CFLAGS+=" -ffloat-store" ;;
+esac
+
 post_patch() {
 	# sse2 is not available on all i686
 	# and it's available on all x86_64