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Matthias Koeppe
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Merge tag '9.3' into t/31338/sage_setup__use_paths_within_sage_local_when_provided_via_sage_conf
SageMath version 9.3, Release Date: 2021-05-09
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‎.github/workflows/tox-experimental.yml

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@@ -38,7 +38,7 @@ jobs:
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fail-fast: false
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max-parallel: 6
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matrix:
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tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
41+
tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
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tox_packages_factor: [maximal]
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targets_pattern: [0-g, h-o, p, q-z]
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env:
@@ -54,15 +54,21 @@ jobs:
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run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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- name: free disk space
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run: |
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df -h
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sudo swapoff -a
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sudo rm -f /swapfile
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sudo apt clean
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sudo apt-get clean
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docker rmi $(docker image ls -aq)
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echo "Largest packages:"
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dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
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sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
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df -h
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- name: Install test prerequisites
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run: |
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sudo DEBIAN_FRONTEND=noninteractive apt-get update
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sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
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sudo apt-get clean
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df -h
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- name: Try to login to docker.pkg.github.com
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# https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
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run: |

‎.github/workflows/tox-gcc_spkg.yml

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@@ -52,15 +52,21 @@ jobs:
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run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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- name: free disk space
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run: |
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df -h
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sudo swapoff -a
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sudo rm -f /swapfile
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sudo apt clean
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sudo apt-get clean
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docker rmi $(docker image ls -aq)
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echo "Largest packages:"
61+
dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
62+
sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
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df -h
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- name: Install test prerequisites
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run: |
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sudo DEBIAN_FRONTEND=noninteractive apt-get update
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sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
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sudo apt-get clean
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df -h
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- name: Try to login to docker.pkg.github.com
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# https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
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run: |

‎.github/workflows/tox-optional.yml

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@@ -38,7 +38,7 @@ jobs:
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fail-fast: false
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max-parallel: 6
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matrix:
41-
tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
41+
tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
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tox_packages_factor: [maximal]
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targets_pattern: [0-g, h-o, p, q-z]
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env:
@@ -56,15 +56,21 @@ jobs:
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run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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- name: free disk space
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run: |
59+
df -h
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sudo swapoff -a
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sudo rm -f /swapfile
61-
sudo apt clean
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sudo apt-get clean
6263
docker rmi $(docker image ls -aq)
64+
echo "Largest packages:"
65+
dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
66+
sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
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df -h
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- name: Install test prerequisites
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run: |
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sudo DEBIAN_FRONTEND=noninteractive apt-get update
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sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
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sudo apt-get clean
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df -h
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- name: Try to login to docker.pkg.github.com
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# https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
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run: |

‎.github/workflows/tox.yml

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@@ -38,7 +38,7 @@ jobs:
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fail-fast: false
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max-parallel: 20
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matrix:
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tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, ubuntu-focal-i386, debian-buster-i386, centos-7-i386]
41+
tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
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tox_packages_factor: [minimal, standard]
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env:
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TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
@@ -52,15 +52,21 @@ jobs:
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run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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- name: free disk space
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run: |
55+
df -h
5556
sudo swapoff -a
5657
sudo rm -f /swapfile
57-
sudo apt clean
58+
sudo apt-get clean
5859
docker rmi $(docker image ls -aq)
60+
echo "Largest packages:"
61+
dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n | tail -n 50
62+
sudo apt-get --fix-broken --yes remove $(dpkg-query -f '${Package}\n' -W | grep -E '^(ghc-|google-cloud-sdk|google-chrome|firefox|mysql-server|dotnet-sdk|hhvm|mono)') || echo "(error ignored)"
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df -h
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- name: Install test prerequisites
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run: |
6266
sudo DEBIAN_FRONTEND=noninteractive apt-get update
6367
sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
68+
sudo apt-get clean
69+
df -h
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- name: Try to login to docker.pkg.github.com
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# https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
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run: |

‎.zenodo.json

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Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
22
"description": "Mirror of the Sage https://sagemath.org/ source tree",
33
"license": "other-open",
4-
"title": "sagemath/sage: 9.3.rc1",
5-
"version": "9.3.rc1",
4+
"title": "sagemath/sage: 9.3",
5+
"version": "9.3",
66
"upload_type": "software",
7-
"publication_date": "2021-03-29",
7+
"publication_date": "2021-05-09",
88
"creators": [
99
{
1010
"affiliation": "SageMath.org",
@@ -15,7 +15,7 @@
1515
"related_identifiers": [
1616
{
1717
"scheme": "url",
18-
"identifier": "https://github.com/sagemath/sage/tree/9.3.rc1",
18+
"identifier": "https://github.com/sagemath/sage/tree/9.3",
1919
"relation": "isSupplementTo"
2020
},
2121
{

‎VERSION.txt

+1-1
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@@ -1 +1 @@
1-
SageMath version 9.3.rc1, Release Date: 2021-03-29
1+
SageMath version 9.3, Release Date: 2021-05-09

‎build/pkgs/brial/spkg-configure.m4

+2-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
SAGE_SPKG_CONFIGURE([brial], [
2-
SAGE_SPKG_DEPCHECK([boost m4ri], [
2+
dnl Trac #31624: Avoid C++ ABI issues
3+
SAGE_SPKG_DEPCHECK([gcc boost m4ri], [
34
# If we're using the system m4ri and boost, ensure that we can
45
# compile and run an executable linked against both libbrial and
56
# libbrial_groebner (both are used by SageMath).

‎build/pkgs/cddlib/checksums.ini

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@@ -1,5 +1,5 @@
11
tarball=cddlib-VERSION.tar.gz
2-
sha1=4bad24b32d9c056615377ff3103e6b95e17628ac
3-
md5=73e5f7dfa72b5c3339c09564721813d6
4-
cksum=3211115816
2+
sha1=8f38597a0479a191a62346dab89794e888c478b6
3+
md5=ec7f35912e34232b5306a643f99b6311
4+
cksum=2420656558
55
upstream_url=https://github.com/cddlib/cddlib/releases/download/VERSION/cddlib-VERSION.tar.gz

‎build/pkgs/cddlib/package-version.txt

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@@ -1 +1 @@
1-
0.94j
1+
0.94m

‎build/pkgs/cddlib/spkg-configure.m4

+26-1
Original file line numberDiff line numberDiff line change
@@ -16,14 +16,39 @@ SAGE_SPKG_CONFIGURE([cddlib], [
1616
AC_CHECK_PROGS(SCDD, [scdd_gmp scdd])
1717
AS_IF([test x$SCDD = x], [sage_spkg_install_cddlib=yes])
1818
19-
dnl Future versions (>= 0.94k) of cddlib will put these headers in
19+
dnl https://trac.sagemath.org/ticket/30319
20+
AS_IF([test -n "$CDDEXEC"], [
21+
AC_MSG_CHECKING([whether $CDDEXEC --redcheck works correctly for real input])
22+
cat > conftest.ine <<EOF
23+
H-representation
24+
linearity 2 1 2
25+
begin
26+
5 4 real
27+
0.0 0.0 1.0 1.0
28+
-1.0 0.0 1.0 1.0
29+
-1.0 2.0 -1.0 0.0
30+
-1.0 4.0 -2.0 0.0
31+
1 0 0 0
32+
end
33+
EOF
34+
rm -f conftest.out
35+
$CDDEXEC --redcheck <conftest.ine >conftest.out 2>& AS_MESSAGE_LOG_FD
36+
AS_IF([grep -q "^Redundant rows.*1" conftest.out 2>& AS_MESSAGE_LOG_FD], [
37+
AC_MSG_RESULT([no])
38+
sage_spkg_install_cddlib=yes
39+
], [
40+
AC_MSG_RESULT([yes])
41+
])
42+
])
43+
dnl Recent versions (>= 0.94k) of cddlib put these headers in
2044
dnl a "cddlib" subdirectory, and Debian currently relocates them
2145
dnl under "cdd". But for now they're at the top-level, in e.g.
2246
dnl /usr/include/cdd.h. The lattE and gfan packages within
2347
dnl SageMath both look for them there, so that's where we have to
2448
dnl check, passing up a chance to detect cddlib on Fedora and Debian
2549
dnl for now. Once all of cddlib's consumers know about the new (or
2650
dnl both) locations, we can update this check to support them.
51+
dnl See https://trac.sagemath.org/ticket/29413
2752
AC_CHECK_HEADER([cdd.h],[],[sage_spkg_install_cddlib=yes],[
2853
#include <setoper.h>
2954
#include <cddmp.h>

‎build/pkgs/cddlib/spkg-install.in

+7
Original file line numberDiff line numberDiff line change
@@ -5,3 +5,10 @@ cd src
55
sdh_configure
66
sdh_make
77
sdh_make_install
8+
9+
# Old versions of cddlib install headers without the official prefix "cddlib/";
10+
# and some distributions install the headers with a prefix "cdd/".
11+
# We install symlinks to shadow possible system installations of these headers.
12+
# This can be removed as soon as all packages that detect cddlib have been
13+
# updated to check the official prefix "cddlib/" first.
14+
(cd $SAGE_DESTDIR$SAGE_LOCAL/include/ && ln -sf cddlib cdd && ln -sf cddlib/*.h .)

‎build/pkgs/configure/checksums.ini

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@@ -1,4 +1,4 @@
11
tarball=configure-VERSION.tar.gz
2-
sha1=df2f6839c4a19b7d21c4f387df24596fcfa2b459
3-
md5=f307be6d68e25b3924cc93d2bcc9dc04
4-
cksum=1158861891
2+
sha1=2d5d2d8a2a6dbc721935f6b3d3ada9a6bd977e19
3+
md5=d84b8fcb2ddd6949d3461f49fae01702
4+
cksum=2508666370

‎build/pkgs/configure/package-version.txt

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@@ -1 +1 @@
1-
6e084f9dbad96c3a166732efb36fe71acd2e7ba2
1+
3f4547f2cc40338ba42329d53f7fb48c31ff9fc8

‎build/pkgs/cvxopt/spkg-install.in

+3-3
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@@ -65,9 +65,9 @@ export CVXOPT_BLAS_LIB="$(cvxopt_output l blas)"
6565
export CVXOPT_BLAS_LIB_DIR="$(pkg-config --variable=libdir blas)"
6666
export CVXOPT_LAPACK_LIB="$(cvxopt_output l lapack)"
6767

68-
if test "x$SAGE_SUITESPARSE_LOCALINSTALL" != "x"; then
69-
export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_LOCAL}"
70-
export CVXOPT_SUITESPARSE_INC_DIR="${SAGE_LOCAL}/include"
68+
if test "x$SAGE_SUITESPARSE_PREFIX" != "x"; then
69+
export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_SUITESPARSE_PREFIX}"
70+
export CVXOPT_SUITESPARSE_INC_DIR="${SAGE_SUITESPARSE_PREFIX}/include"
7171
fi
7272

7373
export CVXOPT_BUILD_GLPK=1

‎build/pkgs/fplll/spkg-configure.m4

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
SAGE_SPKG_CONFIGURE([fplll], [
2-
SAGE_SPKG_DEPCHECK([mpfr], [
2+
SAGE_SPKG_DEPCHECK([gcc mpfr], [
33
dnl If we're using the system mpfr, use pkgconfig to determine
44
dnl if there's a usable system copy of fplll. Unless there's
55
dnl a system that ships fplll without fplll.pc file, falling

‎build/pkgs/fplll/spkg-install.in

+5
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,11 @@ if [ "x$SAGE_DEBUG" = "xyes" ]; then
2020
CONFIGUREFLAGS="$CONFIGUREFLAGS --enable-debug"
2121
fi
2222

23+
if [ -x "$SAGE_LOCAL"/bin/gcc ]; then
24+
# Trac #31624: Avoid C++ ABI issues
25+
CONFIGUREFLAGS="$CONFIGUREFLAGS --without-qd"
26+
fi
27+
2328
export CXXFLAGS="$CXXFLAGS"
2429
export CPPFLAGS="$CPPFLAGS"
2530
export CXX="$CXX"

‎build/pkgs/freetype/checksums.ini

+3-3
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@@ -1,5 +1,5 @@
11
tarball=freetype-VERSION.tar.bz2
2-
sha1=3296b64ad1e7540289f22e4b6383e26e928b0a20
3-
md5=c50a3c9e5e62bdc938a6e1598a782947
4-
cksum=2822306030
2+
sha1=040d6a4be23708132c85ef9df837eb3f8a04c4ab
3+
md5=4934a8b61b636920bcce58e7c7f3e1a2
4+
cksum=2814275332
55
upstream_url=https://download.savannah.gnu.org/releases/freetype/freetype-VERSION.tar.gz

‎build/pkgs/freetype/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
2.10.1
1+
2.10.4

‎build/pkgs/freetype/spkg-configure.m4

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
SAGE_SPKG_CONFIGURE([freetype], [
2-
SAGE_SPKG_DEPCHECK([libpng], [
2+
SAGE_SPKG_DEPCHECK([gcc libpng], [
33
dnl freetype versions are libtool's ones, cf trac #30014
44
PKG_CHECK_MODULES([FREETYPE], [freetype2 >= 16.1], [], [sage_spkg_install_freetype=yes])
55
])

‎build/pkgs/ipywidgets/dependencies

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
$(PYTHON) widgetsnbextension | $(PYTHON_TOOLCHAIN)
1+
$(PYTHON) widgetsnbextension | $(PYTHON_TOOLCHAIN) ipykernel ipython traitlets
22

33
----------
44
All lines of this file are ignored except the first.

‎build/pkgs/libgd/spkg-configure.m4

+3-18
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,6 @@
11
SAGE_SPKG_CONFIGURE([libgd], [
2-
AC_REQUIRE([SAGE_SPKG_CONFIGURE_LIBPNG])
3-
AC_REQUIRE([SAGE_SPKG_CONFIGURE_FREETYPE])
4-
AC_MSG_CHECKING([Installing freetype? ])
5-
if test x$sage_spkg_install_freetype = xyes; then
6-
AC_MSG_RESULT([Yes. Install libgd as well.])
7-
sage_spkg_install_libgd=yes
8-
else
9-
dnl do not just rely on libpng being a dependency of freetype
10-
AC_MSG_CHECKING([Installing libpng? ])
11-
if test x$sage_spkg_install_libpng = xyes; then
12-
AC_MSG_RESULT([Yes. Install libgd as well.])
13-
sage_spkg_install_libgd=yes
14-
else
15-
AC_MSG_RESULT([No.])
2+
dnl Trac #31624: Avoid C++ ABI issues
3+
SAGE_SPKG_DEPCHECK([gcc libpng freetype], [
164
PKG_CHECK_MODULES([LIBGD], [gdlib >= 2.1], [], [sage_spkg_install_libgd=yes])
17-
fi
18-
fi
5+
])
196
])
20-
21-

‎build/pkgs/lrslib/distros/debian.txt

+1
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
lrslib

‎build/pkgs/lrslib/distros/fedora.txt

+1
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@@ -0,0 +1 @@
1+
lrslib

‎build/pkgs/lrslib/distros/freebsd.txt

+1
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@@ -0,0 +1 @@
1+
math/lrslib

‎build/pkgs/lrslib/distros/gentoo.txt

+1
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
sci-libs/lrslib

‎build/pkgs/lrslib/distros/nix.txt

+1
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@@ -0,0 +1 @@
1+
lrs

‎build/pkgs/lrslib/spkg-configure.m4

+7
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
SAGE_SPKG_CONFIGURE([lrslib], [
2+
dnl System lrslib may already be 7.x, which may be compiled with FLINT
3+
SAGE_SPKG_DEPCHECK([gmp mpir flint], [
4+
AC_CHECK_PROGS([LRSNASH], [lrsnash])
5+
AS_IF([test -z "$LRSNASH"], [sage_spkg_install_lrslib=yes])
6+
])
7+
])

‎build/pkgs/ntl/spkg-configure.m4

+2-12
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,7 @@
11
SAGE_SPKG_CONFIGURE([ntl], [
2-
AC_REQUIRE([SAGE_SPKG_CONFIGURE_GMP])
3-
AC_MSG_CHECKING([installing gmp/mpir? ])
4-
if test x$sage_spkg_install_mpir = xyes -o x$sage_spkg_install_gmp = xyes; then
5-
AC_MSG_RESULT([yes; install ntl as well])
6-
sage_spkg_install_ntl=yes
7-
else
8-
AC_MSG_RESULT([no])
9-
fi
10-
112
m4_pushdef(SAGE_NTL_VERSION_MAJOR, [10])
123
m4_pushdef(SAGE_NTL_VERSION_MINOR, [3])
13-
14-
if test x$sage_spkg_install_ntl != xyes; then
4+
SAGE_SPKG_DEPCHECK([gmp mpir gcc], [
155
AC_CHECK_HEADER([NTL/ZZ.h], [], [sage_spkg_install_ntl=yes])
166
AC_MSG_CHECKING([whether we can link a program using NTL])
177
NTL_SAVED_LIBS=$LIBS
@@ -40,7 +30,7 @@ SAGE_SPKG_CONFIGURE([ntl], [
4030
AC_MSG_RESULT([no])
4131
sage_spkg_install_ntl=yes
4232
])
43-
fi
33+
])
4434
4535
m4_popdef([SAGE_NTL_VERSION_MAJOR])
4636
m4_popdef([SAGE_NTL_VERSION_MINOR])

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