forked from mirrors/nixpkgs
Merge pull request #34291 from timokau/sage-fix-shebangs
sage: 8.0 -> 8.1, fix sandbox build
This commit is contained in:
Michael Raskin
GitHub
commit
bfc4d04de7
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@ -18,6 +18,7 @@
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# - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath
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{ stdenv
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, bash
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, fetchurl
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, perl
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, gfortran
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@ -26,13 +27,17 @@
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, gettext
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, which
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, texlive
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, texinfo
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, hevea
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}:
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stdenv.mkDerivation rec {
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version = "8.0";
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version = "8.1";
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name = "sage-${version}";
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# Modified version of patchShebangs that patches to the sage-internal version if possible
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# and falls back to the system version if not.
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patchSageShebangs = ./patchSageShebangs.sh;
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src = fetchurl {
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# Note that the source is *not* fetched from github, since that doesn't
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# the upstream folder with all the source tarballs of the spkgs.
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@ -70,11 +75,12 @@ stdenv.mkDerivation rec {
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"http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz"
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"http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz"
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];
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sha256 = "1a9rhb8jby6fdqa2s7n2fl9jwqqlsl7qz7dbpbwvg6jwlrvni7fg";
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sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq";
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};
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postPatch = ''
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substituteAllInPlace src/bin/sage-env
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bash=${bash} substituteAllInPlace build/bin/sage-spkg
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'';
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installPhase = ''
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@ -84,14 +90,16 @@ stdenv.mkDerivation rec {
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outputs = [ "out" "doc" ];
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buildInputs = [
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bash # needed for the build
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perl # needed for the build
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python # needed for the build
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gfortran # needed to build giac
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gfortran # needed to build giac, openblas
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autoreconfHook # needed to configure sage with prefix
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gettext # needed to build the singular spkg
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hevea # needed to build the docs of the giac spkg
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which # needed in configure of mpir
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# needed to build the docs of the giac spkg
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texinfo # needed to build maxima
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(texlive.combine { inherit (texlive)
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scheme-basic
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collection-pstricks # needed by giac
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@ -102,18 +110,22 @@ stdenv.mkDerivation rec {
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})
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];
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nativeBuildInputs = [ gfortran perl which ];
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patches = [
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# fix usages of /bin/rm
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./spkg-singular.patch
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# help python find the crypt library
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./spkg-python2.patch
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./spkg-python3.patch
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# patches python3 and indirectly python2, since those installation files are symlinked
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./spkg-python.patch
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# fix usages of /usr/bin/perl
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./spkg-git.patch
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# fix usages of /bin/cp and add necessary argument to function call
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./spkg-giac.patch
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# environment
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./env.patch
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# adjust wrapper shebang and patch shebangs after each spkg build
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./shebangs.patch
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];
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enableParallelBuilding = true;
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@ -144,7 +156,14 @@ stdenv.mkDerivation rec {
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preBuild = ''
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# TODO do this conditionally
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export SAGE_SPKG_INSTALL_DOCS='no'
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patchShebangs build
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# symlink python to make sure the shebangs are patched to the sage path
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# while still being able to use python before building it
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# (this is important because otherwise sage will try to install python
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# packages globally later on)
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ln -s "${python}/bin/python2" $out/bin/python2
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ln -s "$out/bin/python2" $out/bin/python
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touch $out/bin/python3
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bash $patchSageShebangs .
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'';
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postBuild = ''
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@ -153,9 +172,12 @@ stdenv.mkDerivation rec {
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rm -rf "$out/sage-root/src/.git"
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rm -r "$out/sage-root/logs"
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# Fix dependency cycle between out and doc
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rm -f "$out/sage-root/config.log"
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rm -f "$out/sage-root/config.status"
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rm -f "$out/sage-root/build/make/Makefile-auto"
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rm -f "$out/sage-home/.sage/gap/libgap-workspace-"*
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# Make sure all shebangs are properly patched
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bash $patchSageShebangs $out
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'';
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# TODO there are some doctest failures, which seem harmless.
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51
pkgs/applications/science/math/sage/patchSageShebangs.sh
Normal file
51
pkgs/applications/science/math/sage/patchSageShebangs.sh
Normal file
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@ -0,0 +1,51 @@
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# This is a slightly modified version of nix's default patchShebangs
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dir="$1"
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echo "patching sage internal script interpreter paths in $( readlink -f "$dir")"
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find "$dir" -type f -perm -0100 | while read f; do
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if [ "$(head -1 "$f" | head -c+2)" != '#!' ]; then
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# missing shebang => not a script
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continue
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fi
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oldInterpreterLine=$(head -1 "$f" | tail -c+3)
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read -r oldPath arg0 args <<< "$oldInterpreterLine"
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if $(echo "$oldPath" | grep -q "/bin/env$"); then
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# Check for unsupported 'env' functionality:
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# - options: something starting with a '-'
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# - environment variables: foo=bar
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if $(echo "$arg0" | grep -q -- "^-.*\|.*=.*"); then
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echo "unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)"
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exit 1
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fi
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executable="$arg0"
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else
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if [ "$oldPath" = "" ]; then
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# If no interpreter is specified linux will use /bin/sh. Set
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# oldpath="/bin/sh" so that we get /nix/store/.../sh.
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oldPath="/bin/sh"
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fi
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executable="$(basename "$oldPath")"
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args="$arg0 $args"
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fi
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newPath="$(echo "$out/bin/$executable $args" | sed 's/[[:space:]]*$//')"
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if [[ ! -x "$newPath" ]] ; then
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newPath="$(command -v "$executable" || true)"
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fi
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# Strip trailing whitespace introduced when no arguments are present
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newInterpreterLine="$(echo "$newPath $args" | sed 's/[[:space:]]*$//')"
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if [ -n "$oldPath" -a "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]; then
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if [ -n "$newPath" -a "$newPath" != "$oldPath" ]; then
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echo "$f: sage interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\""
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# escape the escape chars so that sed doesn't interpret them
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escapedInterpreterLine=$(echo "$newInterpreterLine" | sed 's|\\|\\\\|g')
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sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f"
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fi
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fi
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done
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36
pkgs/applications/science/math/sage/shebangs.patch
Normal file
36
pkgs/applications/science/math/sage/shebangs.patch
Normal file
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@ -0,0 +1,36 @@
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diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
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index 83e61a7e0d..942ba206c7 100755
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--- a/build/bin/sage-spkg
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+++ b/build/bin/sage-spkg
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@@ -648,8 +648,12 @@ if ! sage-apply-patches; then
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error_msg "Error applying patches"
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exit 1
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fi
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+
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+@bash@/bin/bash @patchSageShebangs@ .
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+
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cd ..
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+
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##################################################################
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# The package has been extracted, prepare for installation
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##################################################################
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@@ -671,7 +675,7 @@ write_script_wrapper() {
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local tmpscript="$(dirname "$script")/.tmp-${script##*/}"
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cat > "$tmpscript" <<__EOF__
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-#!/usr/bin/env bash
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+#! @bash@/bin/bash
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export SAGE_ROOT="$SAGE_ROOT"
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export SAGE_SRC="$SAGE_SRC"
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@@ -833,6 +837,9 @@ if [ "$UNAME" = "CYGWIN" ]; then
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sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null
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fi
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+@bash@/bin/bash @patchSageShebangs@ .
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+@bash@/bin/bash @patchSageShebangs@ "$out/bin"
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+
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echo "Successfully installed $PKG_NAME"
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if [ "$SAGE_CHECK" = "yes" ]; then
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13
pkgs/applications/science/math/sage/spkg-python.patch
Normal file
13
pkgs/applications/science/math/sage/spkg-python.patch
Normal file
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@ -0,0 +1,13 @@
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diff --git a/build/pkgs/python3/spkg-build b/build/pkgs/python3/spkg-build
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index 56db087ae5..b450703c5f 100644
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--- a/build/pkgs/python3/spkg-build
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+++ b/build/pkgs/python3/spkg-build
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@@ -27,6 +27,8 @@ fi
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export EXTRA_CFLAGS="`testcflags.sh -Wno-unused` $CFLAGS"
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unset CFLAGS
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+export LDFLAGS="$LDFLAGS -lcrypt"
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+
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if [ "$UNAME" = Darwin ]; then
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PYTHON_CONFIGURE="--disable-toolbox-glue $PYTHON_CONFIGURE"
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@ -1,12 +0,0 @@
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--- old/build/pkgs/python2/spkg-install 2017-07-21 14:10:00.000000000 -0500
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+++ new/build/pkgs/python2/spkg-install 2017-10-15 11:26:54.823134067 -0500
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@@ -22,6 +22,9 @@
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cd src
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+LDFLAGS="-lcrypt $LDFLAGS"
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+export LDFLAGS
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+
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if [ "$SAGE_DEBUG" = "yes" ]; then
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echo "Building Python with pydebug"
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PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug"
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@ -1,12 +0,0 @@
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--- old/build/pkgs/python3/spkg-install 2017-07-21 14:10:00.000000000 -0500
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+++ new/build/pkgs/python3/spkg-install 2017-10-15 13:11:17.769261404 -0500
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@@ -22,6 +22,9 @@
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cd src
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+LDFLAGS="-lcrypt $LDFLAGS"
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+export LDFLAGS
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+
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if [ "$SAGE_DEBUG" = "yes" ]; then
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echo "Building Python with pydebug"
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PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug"
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