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Matthias Koeppe
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Merge tag '9.8.beta1' into t/34268/reduce_r_to_a_dummy_package__upgrade_rpy2
SageMath version 9.8.beta1, Release Date: 2022-09-29
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‎.vscode/settings.json

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@@ -33,5 +33,6 @@
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"Conda",
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"sagemath",
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"Cython"
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]
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],
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"editor.formatOnType": true
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}

‎.zenodo.json

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@@ -1,10 +1,10 @@
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{
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"description": "Mirror of the Sage https://sagemath.org/ source tree",
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"license": "other-open",
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"title": "sagemath/sage: 9.8.beta0",
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"version": "9.8.beta0",
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"title": "sagemath/sage: 9.8.beta1",
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"version": "9.8.beta1",
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"upload_type": "software",
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"publication_date": "2022-09-25",
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"publication_date": "2022-09-29",
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"creators": [
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{
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"affiliation": "SageMath.org",
@@ -15,7 +15,7 @@
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"related_identifiers": [
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{
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"scheme": "url",
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"identifier": "https://github.com/sagemath/sage/tree/9.8.beta0",
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"identifier": "https://github.com/sagemath/sage/tree/9.8.beta1",
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"relation": "isSupplementTo"
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},
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{

‎README.md

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@@ -79,7 +79,7 @@ If your Mac uses the Apple Silicon (M1, arm64) architecture:
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https://brew.sh/ required because it provides a version of ``gfortran`` with
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necessary changes for this platform that are not in a released upstream
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version of GCC. (The ``gfortran`` package that comes with the Sage
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distribution is not suitable for the M1.)
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distribution is not suitable for the M1/M2.)
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If your Mac uses the Intel (x86_64) architecture:
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@@ -184,14 +184,20 @@ in the Installation Guide.
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- Compilers: `gcc`, `gfortran`, `g++` (GCC 8.x to 12.x and recent
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versions of Clang (LLVM) are supported).
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See the Installation Manual for a discussion of suitable compilers.
187+
See [build/pkgs/gcc/SPKG.rst](build/pkgs/gcc/SPKG.rst) and
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[build/pkgs/gfortran/SPKG.rst](build/pkgs/gfortran/SPKG.rst)
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for a discussion of suitable compilers.
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- Build tools: GNU `make`, GNU `m4`, `perl` (including
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``ExtUtils::MakeMaker``), `ranlib`, `git`, `tar`, `bc`.
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See [build/pkgs/_prereq/SPKG.rst](build/pkgs/_prereq/SPKG.rst) for
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more details.
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- Python 3.4 or later, or Python 2.7, a full installation including
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`urllib`; but ideally version 3.8.x, 3.9.x, or 3.10.x, which
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will avoid having to build Sage's own copy of Python 3.
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See [build/pkgs/python3/SPKG.rst](build/pkgs/python3/SPKG.rst)
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for more details.
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We have collected lists of system packages that provide these build
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prerequisites. See, in the folder

‎VERSION.txt

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SageMath version 9.8.beta0, Release Date: 2022-09-25
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SageMath version 9.8.beta1, Release Date: 2022-09-29

‎build/bin/sage-dist-helpers

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@@ -290,6 +290,8 @@ sdh_pip_install() {
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sdh_pip_editable_install() {
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echo "Installing $PKG_NAME (editable mode)"
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# Until https://trac.sagemath.org/ticket/34209 switches us to PEP 660 editable wheels
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export SETUPTOOLS_ENABLE_FEATURES=legacy-editable
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python3 -m pip install --verbose --no-deps --no-index --no-build-isolation --isolated --editable "$@" || \
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sdh_die "Error installing $PKG_NAME"
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}

‎build/make/Makefile.in

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@@ -430,7 +430,7 @@ define SET_SAGE_CHECK
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$(eval SAGE_CHECK_$(1) := $(2))
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endef
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# Set defaults
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$(foreach pkgname, $(NORMAL_PACKAGES),\
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$(foreach pkgname, $(NORMAL_PACKAGES) $(SCRIPT_PACKAGES),\
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$(eval $(call SET_SAGE_CHECK,$(pkgname),$(SAGE_CHECK))))
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# Parsing the SAGE_CHECK_PACKAGES variable:
@@ -460,7 +460,7 @@ $(foreach clause, $(SAGE_CHECK_PACKAGES_sep), \
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$(eval $(call SET_SAGE_CHECK,$(subst ?,,$(clause)),warn)), \
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$(eval $(call SET_SAGE_CHECK,$(clause),yes)))))
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debug-check:
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@echo $(foreach pkgname, $(NORMAL_PACKAGES), SAGE_CHECK_$(pkgname) = $(SAGE_CHECK_$(pkgname)))
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@echo $(foreach pkgname, $(NORMAL_PACKAGES) $(SCRIPT_PACKAGES), SAGE_CHECK_$(pkgname) = $(SAGE_CHECK_$(pkgname)))
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#==============================================================================
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. '$$(SAGE_ROOT)/build/bin/sage-build-env' && \
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SAGE_SPKG_WHEELS=$$($(4))/var/lib/sage/wheels \
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SAGE_INST_LOCAL=$$($(4)) \
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sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log' && \
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sage-logger -p 'SAGE_CHECK=$$(SAGE_CHECK_$(1)) $$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1)-$(2).log' && \
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rm -f "$$($(4))/$(SPKG_INST_RELDIR)/$(1)"-* && \
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touch "$$($(4))/$(SPKG_INST_RELDIR)/$(1)-$(2)"; \
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else ( \

‎build/pkgs/_prereq/SPKG.rst

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Description
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-----------
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This script package represents the minimal requirements (system packages)
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This dummy package represents the minimal requirements (system packages)
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for installing SageMath from source.
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In addition to standard :wikipedia:`POSIX <POSIX>` utilities
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and the :wikipedia:`bash <Bash_(Unix_shell)>` shell,
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the following standard command-line development tools must be installed on your
13+
computer:
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- **make**: GNU make, version 3.80 or later. Version 3.82 or later is recommended.
16+
- **m4**: GNU m4 1.4.2 or later (non-GNU or older versions might also work).
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- **perl**: version 5.8.0 or later.
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- **ar** and **ranlib**: can be obtained as part of GNU binutils.
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- **tar**: GNU tar version 1.17 or later, or BSD tar (as provided on macOS).
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- **python**: Python 3.4 or later, or Python 2.7.
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(This range of versions is a minimal requirement for internal purposes of the SageMath
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build system, which is referred to as ``sage-bootstrap-python``.)
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Other versions of these may work, but they are untested.
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On macOS, suitable versions of all of these tools are provided
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by the Xcode Command Line Tools. To install them, open a terminal
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window and run ``xcode-select --install``; then click "Install" in the
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pop-up window. If the Xcode Command Line Tools are already installed,
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you may want to check if they need to be updated by typing
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``softwareupdate -l``.
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On Linux, ``ar`` and ``ranlib`` are in the `binutils
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<https://www.gnu.org/software/binutils/>`_ package. The other
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programs are usually located in packages with their respective names.
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On Redhat-derived systems not all perl components are installed by
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default and you might have to install the ``perl-ExtUtils-MakeMaker``
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package.
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To check if you have the above prerequisites installed, for example ``perl``,
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type::
43+
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$ command -v perl
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or::
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$ which perl
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on the command line. If it gives an error (or returns nothing), then
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either ``perl`` is not installed, or it is installed but not in your
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:wikipedia:`PATH <PATH_%28variable%29>`.

‎build/pkgs/configure/checksums.ini

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tarball=configure-VERSION.tar.gz
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sha1=c2e1c4db6762c4d97d5127f5f056e46fe3d5a94d
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md5=70dcc35964e4234443c4e77beb2245d7
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cksum=2271434645
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sha1=73f9fe2ad9e2cfe224c7667a784144a1c520b9d8
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md5=8be336b502a66c5a410183be1eca2ca9
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cksum=42655200

‎build/pkgs/configure/package-version.txt

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04fbc829e9850eedf555acc683666c55cb7052d7
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51d49e23f3d3014e301fefcf72bf7a2a3fe0c4e0

‎build/pkgs/distlib/checksums.ini

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tarball=distlib-VERSION.zip
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sha1=e7927ebc964676c17d466ed6a345222c34167a85
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md5=c886b7d99b4085c5d960e7435dcbd397
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cksum=10374426
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upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.zip
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tarball=distlib-VERSION.tar.gz
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sha1=3a86d49dc17320325004564d0dc86afa808624bc
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md5=f60ba4e3f8e76c214d3d00b2227a16f7
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cksum=1543870863
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upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.tar.gz

‎build/pkgs/distlib/package-version.txt

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0.3.4
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0.3.6

‎build/pkgs/gcc/SPKG.rst

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gcc: The GNU Compiler Collection, including the C, C++ and Fortran compiler
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===========================================================================
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gcc: The GNU Compiler Collection or other suitable C and C++ compilers
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======================================================================
33

44
Description
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-----------
66

7-
The GNU Compiler Collection, including the C, C++ and Fortran compiler.
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This package represents the required C and C++ compilers.
8+
9+
- GCC (GNU Compiler Collection) versions 8.x to 12.x are supported.
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- Clang (LLVM) is also supported.
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The required Fortran compiler is represented by the package ``gfortran``.
14+
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You can pass the names of compilers to use to ``./configure`` using
16+
the environment variables :envvar:`CC`, :envvar:`CXX`, and
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:envvar:`FC`, for C, C++, and Fortran compilers, respectively.
18+
19+
For example, if your C compiler is ``clang``, your C++ compiler is
20+
``clang++``, and your Fortran compiler is ``flang``, then you would
21+
need to run::
22+
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$ ./configure CC=clang CXX=clang++ FC=flang
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Vendor and versions of the C and C++ compilers should match.
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Users of older Linux distributions (in particular, ``ubuntu-xenial``
28+
or older, ``debian-stretch`` or older, ``linuxmint-18`` or older)
29+
should upgrade their systems before attempting to install Sage from
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source. Users of ``ubuntu-bionic``, ``linuxmint-19.x``, and
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``opensuse-15.x`` can install a versioned ``gcc`` system package
32+
and then use::
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$ ./configure CC=gcc-8 CXX=g++-8 FC=gfortran-8
35+
36+
or similar. Users on ``ubuntu`` can also install a modern compiler
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toolchain `using the ubuntu-toolchain-r ppa
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<https://askubuntu.com/questions/1140183/install-gcc-9-on-ubuntu-18-04/1149383#1149383>`_.
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On ``ubuntu-trusty``, also the package ``binutils-2.26`` is required;
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after installing it, make it available using ``export
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PATH="/usr/lib/binutils-2.26/bin:$PATH"``. Instead of upgrading their
42+
distribution, users of ``centos-7`` can install a modern compiler
43+
toolchain `using Redhat's devtoolset
44+
<https://stackoverflow.com/a/67212990/557937>`_.
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This package uses the non-standard default
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``configure --with-system-gcc=force``, giving an error at ``configure``
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time when no suitable system compilers are configured.
49+
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You can override this using ``./configure --without-system-gcc``. In
51+
this case, Sage builds and installs the GNU Compiler Collection,
52+
including the C, C++ and Fortran compiler. This is not recommended.
53+
You will need suitable C and C++ compilers from which GCC can
54+
bootstrap itself. There are some known problems with old assemblers,
55+
in particular when building the ``ecm`` and ``fflas_ffpack``
56+
packages. You should ensure that your assembler understands all
57+
instructions for your processor. On Linux, this means you need a
58+
recent version of ``binutils`` (not provided by an SPKG); on macOS
59+
you need a recent version of Xcode.
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61+
(Installing the
62+
``gfortran`` SPKG becomes a no-op in this case.)
63+
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Building Sage from source on Apple Silicon (M1/M2) requires the use of
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Apple's Command Line Tools, and those tools include a suitable
66+
compiler. Sage's ``gcc`` SPKG is not suitable for M1/M2; building it
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will likely fail.
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License
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-------

‎build/pkgs/gfortran/SPKG.rst

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Description
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-----------
66

7-
The GNU Compiler Collection, including the C, C++ and Fortran compiler.
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This particular package is meant to only make gfortran available.
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This package represents the required Fortran compiler.
8+
9+
Officially we support ``gfortran`` from `GNU Compiler Collection (GCC)
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<https://gcc.gnu.org/>`_. It has also been reported that using ``flang``
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(from LLVM) might work.
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You can pass the names of compilers to use to ``./configure`` using
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the environment variables :envvar:`CC`, :envvar:`CXX`, and
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:envvar:`FC`, for C, C++, and Fortran compilers, respectively.
16+
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For example, if your C compiler is ``clang``, your C++ compiler is
18+
``clang++``, and your Fortran compiler is ``flang``, then you would
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need to run::
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$ ./configure CC=clang CXX=clang++ FC=flang
922

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License
1124
-------

‎build/pkgs/hatchling/checksums.ini

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tarball=hatchling-VERSION.tar.gz
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sha1=63ae7f29657e4d069c716e098a9ac8114d2f29f9
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md5=e05f845d94f400c3085bbaab21adcdbe
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cksum=3213522818
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sha1=8f102796a225fb18b0571a44308341c7211d5d94
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md5=c50eff4f711cee451037ec7eb780154a
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cksum=3180958969
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upstream_url=https://pypi.io/packages/source/h/hatchling/hatchling-VERSION.tar.gz

‎build/pkgs/hatchling/package-version.txt

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1.3.1
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1.10.0

‎build/pkgs/importlib_metadata/checksums.ini

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tarball=importlib_metadata-VERSION.tar.gz
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sha1=7d15d8e06299a8f24e076600899aceee75ce8b0b
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md5=a605ba6ec315bc1324fd6b7210fe7c12
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cksum=448954927
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sha1=ec68de1ec1800048de8656b9d211e22b7fe7c53e
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md5=cfcf29185e13439c76d09c94bc8d81f4
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cksum=2134804316
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upstream_url=https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-VERSION.tar.gz

‎build/pkgs/importlib_metadata/package-version.txt

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4.8.2
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4.12.0

‎build/pkgs/importlib_resources/checksums.ini

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tarball=importlib_resources-VERSION.tar.gz
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sha1=d1f2742895a68f3f8d19dd7285df1687877fb15a
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md5=5db738106ca7c05340495c36357986a2
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cksum=1338307365
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sha1=3b4b20fa0399e2fa21c7506be27a4b943495d3ad
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md5=3b6d98270d40b2ba7af1f8d09188f0c2
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cksum=2401793228
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upstream_url=https://pypi.io/packages/source/i/importlib_resources/importlib_resources-VERSION.tar.gz

‎build/pkgs/importlib_resources/package-version.txt

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5.2.2
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5.9.0

‎build/pkgs/jupyter_packaging/checksums.ini

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tarball=jupyter_packaging-VERSION.tar.gz
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sha1=c9b7dd75a70ad6a7c621588db410f07fba7e0fad
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md5=d30e6fb387d46398a3ab26765b8fa74f
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cksum=669146472
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sha1=092d249360aa56838a188decc4bcd09647fda4d9
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md5=9c6834023bd699bda5365ab7ed18bde2
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cksum=3308833189
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upstream_url=https://pypi.io/packages/source/j/jupyter_packaging/jupyter_packaging-VERSION.tar.gz

‎build/pkgs/jupyter_packaging/package-version.txt

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0.12.2
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0.12.3

‎build/pkgs/msolve/SPKG.rst

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msolve: Multivariate polynomial system solver
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=============================================
3+
4+
Description
5+
-----------
6+
7+
Open source C library implementing computer algebra algorithms for solving
8+
polynomial systems (with rational coefficients or coefficients in a prime field).
9+
10+
License
11+
-------
12+
13+
GPL v2+
14+
15+
Upstream Contact
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----------------
17+
18+
https://github.com/algebraic-solving/msolve
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Upstream does not make source tarballs.
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We make tarballs from the fork https://github.com/mkoeppe/msolve (branch 0.4.4+sage)

‎build/pkgs/msolve/checksums.ini

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tarball=msolve-VERSION.tar.gz
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sha1=5b227de8b222bfe8d143e1d7ea77ad71cd209dc8
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md5=2f34bd9ccb089688ae169201281108dc
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cksum=941373315
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upstream_url=https://trac.sagemath.org/raw-attachment/ticket/31664/msolve-VERSION.tar.gz

‎build/pkgs/msolve/dependencies

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$(MP_LIBRARY) flint mpfr
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----------
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All lines of this file are ignored except the first.

‎build/pkgs/msolve/package-version.txt

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0.4.4+sage-2022-09-11

‎build/pkgs/msolve/spkg-install.in

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cd src
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sdh_configure
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sdh_make
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sdh_make_install

‎build/pkgs/msolve/type

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optional

‎build/pkgs/numpy/checksums.ini

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tarball=numpy-VERSION.zip
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sha1=3ac08064b2ec8db8fe4870c2545c9d154f46bb30
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md5=b44849506fbb54cdef9dbb435b2b1987
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cksum=735479084
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upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.zip
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tarball=numpy-VERSION.tar.gz
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sha1=570c995d7b155c7e4ac43bc46594172cedf1e4fa
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md5=6efc60a3f6c1b74c849d53fbcc07807b
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cksum=3973735135
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upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.tar.gz

‎build/pkgs/numpy/package-version.txt

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1.22.4
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1.23.3

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