[patch-2.7.6] Error downloading tarball of patch

[Jianping Pan]

Dear sage dec,

I'm trying to install sagemath on my macOS Sonoma 14.6.1  using git

git clone --origin upstream https://github.com/sagemath/sage.git

and I also ran ./configure Then I ran a few brew commands like

brew install gnupg texinfo cbc igraph apaffenholz/polymake/polymake

brew install flint gsl maxima openblas gpatch singular suite-sparse 

source /Users/jianpingpan/sage/.homebred-build-env

Then I ran make reconfigure

However after I do make, I quickly got the error message (log file attached)

[patch-2.7.6]   File "/Users/jianpingpan/sage/build/bin/../sage_bootstrap/expand_class.py", line 126, in apply

[patch-2.7.6]     function(package_name, *args, **kwds)

[patch-2.7.6]   File "/Users/jianpingpan/sage/build/bin/../sage_bootstrap/app.py", line 329, in download_with_args

[patch-2.7.6]     self.download(package, allow_upstream=allow_upstream)

[patch-2.7.6]   File "/Users/jianpingpan/sage/build/bin/../sage_bootstrap/app.py", line 315, in download

[patch-2.7.6]     package.tarball.download(allow_upstream=allow_upstream)

[patch-2.7.6]   File "/Users/jianpingpan/sage/build/bin/../sage_bootstrap/tarball.py", line 187, in download

[patch-2.7.6]     raise FileNotMirroredError('tarball does not exist on mirror network and neither at the upstream URL')

[patch-2.7.6] sage_bootstrap.tarball.FileNotMirroredError: tarball does not exist on mirror network and neither at the upstream URL

[patch-2.7.6] ************************************************************************

[patch-2.7.6] Error downloading tarball of patch

[patch-2.7.6] ************************************************************************

[patch-2.7.6] Please email sage-devel (http://groups.google.com/group/sage-devel)

[patch-2.7.6] explaining the problem and including the log files

[patch-2.7.6]   /Users/jianpingpan/sage/logs/pkgs/patch-2.7.6.log

[patch-2.7.6] and

[patch-2.7.6]   /Users/jianpingpan/sage/config.log

[patch-2.7.6] Describe your computer, operating system, etc.

[patch-2.7.6] ************************************************************************

make[2]: *** [patch-SAGE_LOCAL-no-deps] Error 1

make[1]: *** [/Users/jianpingpan/sage/local/var/lib/sage/installed/patch-2.7.6] Error 2

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make base-toolchain'):

* package:         patch-2.7.6

  last build time: Apr 13 08:30

  log file:        /Users/jianpingpan/sage/logs/pkgs/patch-2.7.6.log

It is safe to delete any log files and build directories, but they

contain information that is helpful for debugging build problems.

WARNING: If you now run 'make' again, the build directory of the

same version of the package will, by default, be deleted. Set the

environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make: *** [base-toolchain] Error 1

I tried the method in https://groups.google.com/g/sage-devel/c/_cotG4ONZeY/m/oIM0k21gCQAJ but still have the same issue.

Thanks!

[Dima Pasechnik]

While you can download the tarfile from
https://ftp.gnu.org/gnu/patch/patch-2.7.6.tar.gz into upstream/
it's more economic to use Homebrew for patch, and many more dependencies.

PS. I gather that macOS patch is good enough nowadays, and we can use
it, as proposed on https://github.com/sagemath/sage/issues/30481

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[John H Palmieri]

It seems that the most recent version of patch in homebrew no longer provides automatic access to a binary "patch" (which I think it used to do); instead it says

    If you need to use it as "patch", you can add a "gnubin" directory
    to your PATH from your bashrc like:

        PATH="/opt/homebrew/opt/gpatch/libexec/gnubin:$PATH"

If I make that change to PATH, then I see

% patch --version                            
GNU patch 2.8
Copyright 1989-2025 Free Software Foundation, Inc.
Copyright 1984-1988 Larry Wall

but Sage doesn't find it and insists on building its own patch. The top-level config.log file shows that this directory is in PATH, but it says

## ------------------------------------------------------ ##
## Checking whether SageMath should install SPKG patch... ##
## ------------------------------------------------------ ##
real_configure:46409: checking for GNU patch >= 2.7.0
real_configure:46495: result:
real_configure:46521: no suitable system package found for SPKG patch

[Dima Pasechnik]

On Mon, Apr 14, 2025 at 12:33 PM John H Palmieri <jhpalm...@gmail.com> wrote:

It seems that the most recent version of patch in homebrew no longer provides automatic access to a binary "patch" (which I think it used to do); instead it says

    If you need to use it as "patch", you can add a "gnubin" directory
    to your PATH from your bashrc like:

        PATH="/opt/homebrew/opt/gpatch/libexec/gnubin:$PATH"

If I make that change to PATH, then I see

% patch --version                            
GNU patch 2.8
Copyright 1989-2025 Free Software Foundation, Inc.
Copyright 1984-1988 Larry Wall

but Sage doesn't find it and insists on building its own patch. The top-level config.log file shows that this directory is in PATH, but it says

## ------------------------------------------------------ ##
## Checking whether SageMath should install SPKG patch... ##
## ------------------------------------------------------ ##
real_configure:46409: checking for GNU patch >= 2.7.0
real_configure:46495: result:
real_configure:46521: no suitable system package found for SPKG patch

the macro in spkg-configure doesn't correctly check that 2.8 >= 2.7.0 because it does not match only 2 numeric fields.

e.g.

$ patch --version | sed -n -e 's/GNU patch *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'
2.7.6.211-86ac

$

$ echo "GNU patch 2.8"| sed -n -e 's/GNU patch *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p' # no output!

$

$ echo "GNU patch 2.8.42 "| sed -n -e 's/GNU patch *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'
2.8.42

This ought to be fixed.

See https://github.com/sagemath/sage/issues/39941

Dima

To view this discussion visit https://groups.google.com/d/msgid/sage-devel/1218a0a7-f769-4eaf-8342-622e8781bcd6n%40googlegroups.com.

[Jianping Pan]

Hi all,

Sorry for the  late reply. I tried many things and was not able to fix it. However, I was able to install sage using Conda which was a painless process!

In case it is helpful for anyone, below was what worked for me:

(1) Install conda in the terminal. I used Charlie Parker's new answer using only the terminal for mac zsh from https://stackoverflow.com/questions/49118277/what-is-the-best-way-to-install-conda-on-macos-apple-mac

(2) Install sage using Conda https://doc.sagemath.org/html/en/installation/conda.html

conda config --add channels conda-forge

conda config --set channel_priority strict

conda create -n sageenv sage python=3.12

(3) activate sageenv environment in conda

conda activate /Users/jianping.pan/anaconda3/envs/sageenv

(4) Install some optional packages, after activating the above environment

conda install pynormaliz

sage -pip install multipolynomial_bases

sage -pip install jupyterlab

(5) run sage from jupyterlab

sage -n jupyterlab

Best,

Jianping