Package Details: macaulay2 19030.995c6fd8c-1

Git Clone URL: https://aur.archlinux.org/macaulay2.git (read-only, click to copy)
Package Base: macaulay2
Description: Software system for algebraic geometry and commutative algebra
Upstream URL: http://www.math.uiuc.edu/Macaulay2/
Licenses: GPL
Submitter: remyoudompheng
Maintainer: ConnorBehan
Last Packager: ConnorBehan
Votes: 7
Popularity: 0.56
First Submitted: 2009-04-09 17:09 (UTC)
Last Updated: 2024-04-04 17:04 (UTC)

Latest Comments

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lutuputu commented on 2024-03-09 11:45 (UTC)

I face the same error as @ghbrown does.

ghbrown commented on 2024-02-19 21:02 (UTC)

I face the following issue when trying to install.

+ make -j1 prefix=/home/ghbrown/.cache/yay/macaulay2/src/M2/M2/usr-host
make[3]: Entering directory '/home/ghbrown/.cache/yay/macaulay2/src/M2/M2/libraries/nauty/build/nauty27b11'
gcc -c -std=gnu11 -march=x86-64 -mtune=generic -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g3 -O2 -w  -mpopcnt -o naututil.o naututil.c
In file included from naututil.h:119,
                 from naututil.c:84:
nauty.h:43:23: error: operator '==' has no left operand
   43 | #if _FILE_OFFSET_BITS == 64
      |                       ^~
make[3]: *** [makefile:99: naututil.o] Error 1

When grepping I found some lines where it should be automatically detected and set via flags, but somehow that's not happening and the comparison fails.

curranmc commented on 2023-03-14 21:15 (UTC)

Hi Connor, can you please remove pr2536.patch from this package? It is currently broken, since that PR was merged here: https://github.com/Macaulay2/M2/pull/2536

To any other users: in the meantime, you can make this package work by commenting out line 22, which reads patch -Np1 -i ../pr2536.patch.

fish-monster commented on 2022-11-14 10:58 (UTC) (edited on 2022-11-14 11:05 (UTC) by fish-monster)

I come across the following error when building:

 + rm -f '/home/my-name/macaulay2/src/M2/M2/usr-host/lib/*.la'
/usr/bin/install -c -d /home/my-name/macaulay2/src/M2/M2/usr-host/bin
/usr/bin/install: cannot create directory ‘/home/my-name/macaulay2/src/M2/M2/usr-host/bin’: File exists
make[2]: *** [../Makefile.library:135: .installed-6.2.0] Error 1
make[2]: Leaving directory '/home/my-name/macaulay2/src/M2/M2/libraries/csdp'
make[1]: *** [Makefile:7: all-in-csdp] Error 2
make[1]: Leaving directory '/home/my-name/macaulay2/src/M2/M2/libraries'
make: *** [GNUmakefile:251: all-in-libraries] Error 2
make: Leaving directory '/home/my-name/macaulay2/src/M2/M2'
==> ERROR: A failure occurred in build().
    Aborting...

Removing the file bin and rerunning it does not change anything. Removing everything and starting from anew also not.

halun commented on 2022-08-06 10:19 (UTC)

OK. Thanks.

ConnorBehan commented on 2022-08-05 21:44 (UTC)

Alright, the PKGBUILD now applies the patch you mention. The config file with $srcdir is something that would only be used if you tried to write a program depending on M2. But maybe the warning will go away if you install fflas-ffpack from [community] before starting the build.

halun commented on 2022-08-05 10:38 (UTC) (edited on 2022-08-05 10:38 (UTC) by halun)

At the end of the build process, I got the following message:

==> WARNING: Package contains reference to $srcdir

The command

grep -R "$PWD/src" pkg/

suggested by the Arch Wiki in this situation lists the following 25 binaries:

grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libgccpp.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int64.so.0.0.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libgccpp.so.1: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libzsolve.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2gmp.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libcord.so.1.4.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int32.so.0.0.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2gmp.so.0.0.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int32.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libzsolve.so.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2gmp.so.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libcord.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int64.so.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libgccpp.so.1.4.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libzsolve.so.0.0.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int32.so.0: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/libcord.so.1: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/lib/lib4ti2int64.so: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/output: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/gensymm: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/genmodel: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/4ti2int32: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/4ti2gmp: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/zsolve: binary file matches
grep: pkg/macaulay2/usr/lib/Macaulay2/Macaulay2/bin/4ti2int64: binary file matches

And it also finds a match in one text file, namely the one which after package installation ends up at

/usr/lib/Macaulay2/Macaulay2/bin/fflas-ffpack-config

starting with the lines

prefix=/home/hans/src/macaulay2/src/M2/M2/usr-host
exec_prefix=${prefix}
includedir=${prefix}/include
libdir=${exec_prefix}/lib

This clearly seems completely wrong. Does anyone know what the intended 'prefix' directory is, and how to correct this (including the binary files, if they are also problematic)?

halun commented on 2022-08-05 10:26 (UTC) (edited on 2022-08-05 10:38 (UTC) by halun)

I was able to work around the CotangentSchubert build error mentioned in previous comments, by manually applying the fix from https://github.com/Macaulay2/M2/pull/2536/files (using the substitution trick courtesy of https://superuser.com/a/802490). Like this: after the 'sed' lines in the 'build()' section of the PKGBUILD, add the lines

  FIND='for (int i = 0; i < nvars_; i++) heft_degree_of_var_->array[i] = 1;' REPLACE='for (int i = 0; i < nvars_; i++)
        {
          monomial m = degree_monoid_->make_one();
          degree_monoid_->from_expvector(t, m);
          degree_of_var_.push_back(m);
          heft_degree_of_var_->array[i] = 1;
        }' ruby -p -i -e "gsub(ENV['FIND'], ENV['REPLACE'])" Macaulay2/e/monoid.cpp

By the way, I also removed the 'frobby' dependency, and replaced 'singular-factory' with 'singular', and it seems to have worked fine.

Alad commented on 2022-07-03 17:18 (UTC) (edited on 2022-07-03 18:56 (UTC) by Alad)

This builds fine with gcc 12.1

Also, why fix make -j1? The compilation is pretty slow because of it.

edit: the build failed after several hours :-(

-- making example results for "basisCoeffs"                                
 ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512;  cd /tmp/M2-2665038-0/1-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/usr-dist/x86_64-Linux-Arch-rolling/bin/M2-binary" -q --int --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("CotangentSchubert",Reload=>true,FileName=>"/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/Macaulay2/packages/CotangentSchubert.m2")' <"/tmp/M2-2665038-0/0_basis__Coeffs.m2" >>"/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/usr-dist/common/share/doc/Macaulay2/CotangentSchubert/example-output/_basis__Coeffs.errors" 2>&1
/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/usr-dist/common/share/doc/Macaulay2/CotangentSchubert/example-output/_basis__Coeffs.errors:0:1: (output file) error: Macaulay2 killed by signal 6
/tmp/M2-2665038-0/0_basis__Coeffs.m2:0:1: (input file)
M2: *** Error 6
 -- 1.8018 seconds elapsed
 -- making example results for "segreClass"                                  -- 0.457452 seconds elapsed
 -- making example results for "setupCotangent"                              -- 0.418435 seconds elapsed
 -- making example results for "chernClass"                                  -- 0.444176 seconds elapsed
 -- making example results for "puzzle"                                      -- 0.396112 seconds elapsed
 -- warning: installPackage: 1 error(s) occurred running examples for package CotangentSchubert
/usr/include/c++/12.1.0/bits/stl_vector.h:1142: std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = const int*; _Alloc = gc_allocator<const int*>; const_reference = const int* const&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
make[2]: *** [Makefile:100: /home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/usr-dist/x86_64-Linux-Arch-rolling/lib/Macaulay2/CotangentSchubert/.installed] Aborted (core dumped)
make[2]: Leaving directory '/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/Macaulay2/packages'
make[1]: *** [Makefile:15: all-in-packages] Error 2
make[1]: Leaving directory '/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2/Macaulay2'
make: *** [GNUmakefile:251: all-in-Macaulay2] Error 2
make: Leaving directory '/home/archie/.cache/aurutils/sync/macaulay2/src/M2/M2'
==> ERROR: A failure occurred in build().
    Aborting...

DanGrayson commented on 2022-06-28 13:58 (UTC)

We've had givaro listed in the INSTALL file for Arch Linux since 2016-08-20; I hope we can get issue #2513 resolved soon.