diff --git a/pkgs/applications/science/math/gap/default.nix b/pkgs/applications/science/math/gap/default.nix index 3b3d8a58b56..c309423f142 100644 --- a/pkgs/applications/science/math/gap/default.nix +++ b/pkgs/applications/science/math/gap/default.nix @@ -1,7 +1,6 @@ { stdenv , lib , fetchurl -, fetchpatch , makeWrapper , readline , gmp @@ -35,7 +34,7 @@ let "autpgrp-*" "alnuth-*" "crisp-*" - "ctbllib" + "ctbllib-*" "FactInt-*" "fga" "irredsol-*" @@ -62,11 +61,11 @@ in stdenv.mkDerivation rec { pname = "gap"; # https://www.gap-system.org/Releases/ - version = "4.11.0"; + version = "4.11.1"; src = fetchurl { - url = "https://files.gap-system.org/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2"; - sha256 = "sha256-vwcKENwqxgWT/mXfD4c9ctTWdQHobrJipva9SPyGhgI="; + url = "https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz"; + sha256 = "sha256-ZjXF2n2CdV+DOUhrnKwzdm9YcS8pfoI0+6QIGJAuowQ="; }; # remove all non-essential packages (which take up a lot of space) @@ -84,23 +83,6 @@ stdenv.mkDerivation rec { makeWrapper ]; - patches = [ - # Fix for locale specific tests causing issues. Already upstream. - # Backport of https://github.com/gap-system/gap/pull/4022 - (fetchpatch { - name = "remove-locale-specific-tests.patch"; - url = "https://github.com/gap-system/gap/commit/c18b0c4215b5212a2cc4f305e2d5b94ba716bee8.patch"; - sha256 = "sha256-De+T9Y7ewRT6plJrj2VR8axRvD/JCTYKOBWB7Bw0oq0="; - }) - - # fixes aarch64 gc crashes: https://github.com/gap-system/gap/pull/3965 - (fetchpatch { - name = "mark-genstackfuncbags-as-noinline.patch"; - url = "https://github.com/gap-system/gap/commit/f0a8f49ff8dad0a5fa77253d45457c6f40f96778.patch"; - sha256 = "sha256-GU9tOP1stX2vn8m8kXOBupEpxIYArA76ibKL8eLn0MY="; - }) - ]; - # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min. # tests are run twice, once with all packages loaded and once without # checkTarget = "teststandard"; diff --git a/pkgs/applications/science/math/gap/mark-genstackfuncbags-as-noinline.patch b/pkgs/applications/science/math/gap/mark-genstackfuncbags-as-noinline.patch deleted file mode 100644 index 3a2f7231c09..00000000000 --- a/pkgs/applications/science/math/gap/mark-genstackfuncbags-as-noinline.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/gasman.c b/src/gasman.c -index 417811401..314a74190 100644 ---- a/src/gasman.c -+++ b/src/gasman.c -@@ -1861,7 +1861,7 @@ void SparcStackFuncBags( void ) - #endif - - --void GenStackFuncBags ( void ) -+NOINLINE void GenStackFuncBags ( void ) - { - Bag * top; /* top of stack */ - Bag * p; /* loop variable */ diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix index 9cdcd2b9ea3..54e26cd2ee8 100644 --- a/pkgs/applications/science/math/pynac/default.nix +++ b/pkgs/applications/science/math/pynac/default.nix @@ -22,23 +22,44 @@ stdenv.mkDerivation rec { }; patches = [ - (fetchpatch { - name = "handle_factor.patch"; - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3.rc3"; - sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw="; - }) + # the five patches below are included with sage 9.3. since pynac + # is a self-described "Sage Math support library", we include them + # here. + # https://trac.sagemath.org/ticket/30688 (fetchpatch { name = "power_inf_loop.patch"; - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3.rc3"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3"; sha256 = "sha256-VYeaJl8u2wl7FQ/6xnpZv1KpdNYEmJoPhuMrBADyTRs="; }) + # https://trac.sagemath.org/ticket/31479 + (fetchpatch { + name = "disable_poly_mul_expand.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/disable_poly_mul_expand.patch?h=9.3"; + sha256 = "sha256-gRjoltU9Tzj7fjNyE25fY+iyDxERzSTOMigzxFpUqPo="; + }) + + # https://trac.sagemath.org/ticket/31530 (fetchpatch { name = "too_much_sub.patch"; - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3.rc3"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3"; sha256 = "sha256-lw7xSQ/l+rzPu+ghWF4omYF0mKksGGPuuHJTktvbdis="; }) + + # https://trac.sagemath.org/ticket/31554 + (fetchpatch { + name = "handle_factor.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3"; + sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw="; + }) + + # https://trac.sagemath.org/ticket/31645 + (fetchpatch { + name = "seriesbug.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/seriesbug.patch?h=9.3"; + sha256 = "sha256-b3//oirN7JHDYqrvE+tDYcnKpSYQJ08yBzcNlII2Dts="; + }) ]; buildInputs = [ diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 91e855777f0..ecbda8f239a 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -24,14 +24,14 @@ let ); in stdenv.mkDerivation rec { - version = "9.3.rc4"; + version = "9.3"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-LDY07By2j6JagkgT9zeDJ93+m2/oXXEnDRTDzmR8ftk="; + sha256 = "sha256-l9DX8jcDdKA7GJ6xU+nBsmlZxrcZ9ZUAJju621ooBEo="; }; # Patches needed because of particularities of nix or the way this is packaged. diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 695af3d1744..df298aab211 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -31,11 +31,9 @@ stdenv.mkDerivation rec { owner = "Singular"; repo = "Singular"; - # 4.2.0p2 is not tagged, but the tarball matches commit - # 6f68939ddf612d96e3caaaaa8275f77613ac1da8. the commit below has - # two extra fixes. - rev = "3cda50c00a849455efa2502e56596955491a353a"; - sha256 = "sha256-OizPhGE6L2LTOrKfeDdDB6BSdvYkDVXvbbYjV14hnHM="; + # 4.2.0p2 is not tagged, but the tarball matches the commit below. + rev = "6f68939ddf612d96e3caaaaa8275f77613ac1da8"; + sha256 = "sha256-BJNzYylzDqD/5YjzjxPRb/c96tYiuGy9Y+A7qf3ZSG8="; # if a release is tagged it will be in the format below. # rev = "Release${lib.replaceStrings ["."] ["-"] version}"; @@ -60,6 +58,13 @@ stdenv.mkDerivation rec { # https://github.com/alsa-project/alsa-firmware/issues/3 for a # related issue. ./use-older-ax-prog-cc-for-build.patch + + # https://github.com/Singular/Singular/issues/1086 + (fetchpatch { + name = "schubert-lib-fails-with-too-many-cpus.patch"; + url = "https://github.com/Singular/Singular/commit/3cda50c00a849455efa2502e56596955491a353a.patch"; + sha256 = "sha256-fgYd+2vT32w5Ki8kKx6PfZn2e4QSJcYWOwEFXtc+lSA="; + }) ] ++ lib.optionals enableDocs [ # singular supports building without 4ti2, bertini, normaliz or # topcom just fine, but the docbuilding does not skip manual pages @@ -67,6 +72,13 @@ stdenv.mkDerivation rec { # doc2tex.pl::HandleLib, since it seems to ignore "-exclude" # argumens). skip them manually. ./disable-docs-for-optional-unpackaged-deps.patch + + # fix some non-ascii characters in doc/decodegb.doc + (fetchpatch { + name = "decodegb-ascii.patch"; + url = "https://github.com/Singular/Singular/commit/36966d9009de572ee4dbc487f3e5744098fe91be.patch"; + sha256 = "sha256-9WcEov/oOQRC584ag6WVHFwY2aCjbM75HWyvZoEwppw="; + }) ]; configureFlags = [ @@ -83,9 +95,6 @@ stdenv.mkDerivation rec { substituteInPlace Tst/regress.cmd --replace 'mysystem_catch("hostname")' 'nix_test_runner' patchShebangs . - '' + lib.optionalString enableDocs '' - # work around encoding problem - sed -i -e 's/\xb7/@cdot{}/g' doc/decodegb.doc ''; # For reference (last checked on commit 75f460d): @@ -149,7 +158,7 @@ stdenv.mkDerivation rec { # singular tests are a bit complicated, see # https://github.com/Singular/Singular/tree/spielwiese/Tst - # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773 + # https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773 testsToRun = [ "Old/universal.lst" "Buch/buch.lst" @@ -181,7 +190,7 @@ stdenv.mkDerivation rec { 2>"$TMPDIR/out-err.log" # unfortunately regress.cmd always returns exit code 0, so check stderr - # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773 + # https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773 if [[ -s "$TMPDIR/out-err.log" ]]; then cat "$TMPDIR/out-err.log" exit 1 diff --git a/pkgs/data/misc/graphs/default.nix b/pkgs/data/misc/graphs/default.nix index 19438d83566..93a0d75aaf6 100644 --- a/pkgs/data/misc/graphs/default.nix +++ b/pkgs/data/misc/graphs/default.nix @@ -7,9 +7,7 @@ stdenv.mkDerivation rec { version = "20210214"; src = fetchurl { - url = "https://mirrors.mit.edu/sage/spkg/upstream/${pname}/${pname}-${version}.tar.bz2"; - # TODO: switch to the url below once Sage 9.3 is released - # url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2"; + url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2"; sha256 = "sha256-ByN8DZhTYRUFw4n9e7klAMh0P1YxurtND0Xf2DMvN0E="; };