testing/julia: new abuild

http://julialang.org/
A high-level, high-performance dynamic language for technical computing.

10 files changed, 479 insertions, 0 deletions

diff --git a/testing/julia/0001-hardened.patch b/testing/julia/0001-hardened.patch
new file mode 100644
index 0000000000..2984356c7b
--- /dev/null
+++ b/testing/julia/0001-hardened.patch
@@ -0,0 +1,29 @@
+From: Jakub Jirutka <jakub@jirutka.cz>
+Date: Sun, 05 Jun 2016 14:11:00 +0200
+Subject: [PATCH] Disable PaX memory protection for julia binary
+--- a/Makefile
++++ b/Makefile
+@@ -71,7 +71,13 @@
+ julia-sysimg-debug : julia-inference julia-ui-debug
+ 	@$(MAKE) $(QUIET_MAKE) $(build_private_libdir)/sys-debug.$(SHLIB_EXT) JULIA_BUILD_MODE=debug
+ 
+-julia-debug julia-release : julia-% : julia-ui-% julia-sysimg-% julia-symlink julia-libccalltest
++julia-pax-release : julia-ui-release
++	paxmark m $(JULIA_EXECUTABLE_release)
++
++julia-pax-debug : julia-ui-debug
++	paxmark m $(JULIA_EXECUTABLE_debug)
++
++julia-debug julia-release : julia-% : julia-ui-% julia-pax-% julia-sysimg-% julia-symlink julia-libccalltest
+ 
+ debug release : % : julia-%
+ 
+@@ -527,7 +533,7 @@
+ 	test testall testall1 test clean distcleanall cleanall clean-* \
+ 	run-julia run-julia-debug run-julia-release run \
+ 	install binary-dist light-source-dist.tmp light-source-dist \
+-	dist full-source-dist source-dist
++	dist full-source-dist source-dist julia-pax-release julia-pax-debug
+ 
+ test: check-whitespace $(JULIA_BUILD_MODE)
+ 	@$(MAKE) $(QUIET_MAKE) -C test default JULIA_BUILD_MODE=$(JULIA_BUILD_MODE)
diff --git a/testing/julia/0002-verbose-build.patch b/testing/julia/0002-verbose-build.patch
new file mode 100644
index 0000000000..49bb036996
--- /dev/null
+++ b/testing/julia/0002-verbose-build.patch
@@ -0,0 +1,17 @@
+Description: Ensure that build is verbose
+Author: Sébastien Villemot <sebastien@debian.org>
+Forwarded: not-needed
+Last-Update: 2013-10-09
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/deps/Makefile
++++ b/deps/Makefile
+@@ -756,7 +756,7 @@
+ 	touch -c $(LIBUV_SRC_DIR)/Makefile.in
+ 	touch -c $(LIBUV_SRC_DIR)/configure
+ 	cd $(LIBUV_SRC_DIR) && \
+-	./configure --with-pic $(CONFIGURE_COMMON) $(UV_FLAGS)
++	./configure --with-pic $(CONFIGURE_COMMON) $(UV_FLAGS) --disable-silent-rules
+ 	touch -c $@
+ $(UV_SRC_TARGET): $(LIBUV_SRC_DIR)/config.status
+ 	$(MAKE) -C $(LIBUV_SRC_DIR) $(UV_MFLAGS)
diff --git a/testing/julia/0003-no-clean-docs.patch b/testing/julia/0003-no-clean-docs.patch
new file mode 100644
index 0000000000..7046ea34a2
--- /dev/null
+++ b/testing/julia/0003-no-clean-docs.patch
@@ -0,0 +1,18 @@
+--- a/Makefile
++++ b/Makefile
+@@ -495,7 +493,6 @@
+ 
+ clean: | $(CLEAN_TARGETS)
+ 	@$(MAKE) -C base clean
+-	@$(MAKE) -C doc clean
+ 	@$(MAKE) -C src clean
+ 	@$(MAKE) -C ui clean
+ 	@$(MAKE) -C test clean
+@@ -517,7 +514,6 @@
+ 
+ distcleanall: cleanall
+ 	@$(MAKE) -C deps distcleanall
+-	@$(MAKE) -C doc cleanall
+ 	rm -fr $(build_prefix) $(build_staging)
+ 
+ .PHONY: default debug release check-whitespace release-candidate \
diff --git a/testing/julia/0004-remove-sysctl.h.patch b/testing/julia/0004-remove-sysctl.h.patch
new file mode 100644
index 0000000000..42c71cb893
--- /dev/null
+++ b/testing/julia/0004-remove-sysctl.h.patch
@@ -0,0 +1,33 @@
+From 6f09a6de41e7e35779e0755d9e52a4bf79424109 Mon Sep 17 00:00:00 2001
+From: albap <albapompeo@gmail.com>
+Date: Sun, 31 Jan 2016 10:50:02 -0200
+Subject: [PATCH] Remove nonstandard header sys/sysctl.h
+
+This header prevents me from building Julia on musl libc.
+
+```
+/home/alba/julia/src/sys.c:16:24: fatal error: sys/sysctl.h: No such file or directory
+compilation terminated.
+Makefile:94: recipe for target 'sys.o' failed
+make[1]: *** [sys.o] Error 1
+```
+
+If I remove it from julia/src/sys.c then it works.
+
+Why is sys/sysctl.h needed in first place? I cannot find it in POSIX.
+---
+ src/sys.c | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/src/sys.c b/src/sys.c
+index 9a48871..89069a9 100644
+--- a/src/sys.c
++++ b/src/sys.c
+@@ -13,7 +13,6 @@
+ #ifdef _OS_WINDOWS_
+ #include <psapi.h>
+ #else
+-#include <sys/sysctl.h>
+ #include <sys/wait.h>
+ #include <sys/ptrace.h>
+ #include <unistd.h>
diff --git a/testing/julia/0005-llvm-3.8.patch b/testing/julia/0005-llvm-3.8.patch
new file mode 100644
index 0000000000..c301f964c2
--- /dev/null
+++ b/testing/julia/0005-llvm-3.8.patch
@@ -0,0 +1,56 @@
+Description: LLVM 3.8 compatibility
+ These fixes come straight from upstream's git.
+Origin: Upstream, https://github.com/JuliaLang/julia/commit/b67609b988febe062e6709d8972c4f869c82cfc0
+Origin: Upstream, https://github.com/JuliaLang/julia/commit/3f6abadc9d12bb9d59ec775db4277b3841395d0b
+Origin: Upstream, https://github.com/JuliaLang/julia/commit/caf3c74426696d43101d9607b1a2cd3a5e05bc0f
+Author: Graham Inggs <ginggs@debian.org>
+Last-Update: 2016-02-03
+--- a/src/cgutils.cpp
++++ b/src/cgutils.cpp
+@@ -219,7 +219,11 @@
+         }
+     }
+ 
++#ifdef LLVM38
++    virtual Value *materializeDeclFor(Value *V)
++#else
+     virtual Value *materializeValueFor (Value *V)
++#endif
+     {
+         Function *F = dyn_cast<Function>(V);
+         if (F) {
+@@ -492,7 +496,11 @@
+ 
+     // now copy the module, since PM.run may modify it
+     ValueToValueMapTy VMap;
++#ifdef LLVM38
++    Module *clone = CloneModule(shadow_module, VMap).release();
++#else
+     Module *clone = CloneModule(shadow_module, VMap);
++#endif
+ #ifdef LLVM37
+     // Reset the target triple to make sure it matches the new target machine
+     clone->setTargetTriple(TM->getTargetTriple().str());
+--- a/src/intrinsics.cpp
++++ b/src/intrinsics.cpp
+@@ -780,12 +780,20 @@
+              jl_options.fast_math == JL_OPTIONS_FAST_MATH_ON)) {
+             FastMathFlags fmf;
+             fmf.setUnsafeAlgebra();
++#ifdef LLVM38
++            builder.setFastMathFlags(fmf);
++#else
+             builder.SetFastMathFlags(fmf);
++#endif
+         }
+     }
+     IRBuilder<>& operator()() const { return builder; }
+     ~math_builder() {
++#ifdef LLVM38
++        builder.setFastMathFlags(old_fmf);
++#else
+         builder.SetFastMathFlags(old_fmf);
++#endif
+     }
+ };
+ 
diff --git a/testing/julia/0006-fix-contrib-install.patch b/testing/julia/0006-fix-contrib-install.patch
new file mode 100644
index 0000000000..f41746586b
--- /dev/null
+++ b/testing/julia/0006-fix-contrib-install.patch
@@ -0,0 +1,32 @@
+From 2298cb0e5158fe0edc58afdb6a06c8b2d5ae4092 Mon Sep 17 00:00:00 2001
+From: Tony Kelman <tony@kelman.net>
+Date: Mon, 6 Jun 2016 10:40:01 -0700
+Subject: [PATCH] fix contrib/install.sh when using busybox awk
+
+```
+/ # echo foobar | busybox awk '{print substr($0, 2, length-2)}'
+awk: cmd. line:1: Unexpected token
+/ # echo foobar | busybox awk '{print substr($0, 2, length($0)-2)}'
+ooba
+/ # echo foobar | gawk '{print substr($0, 2, length-2)}'
+ooba
+/ # echo foobar | gawk '{print substr($0, 2, length($0)-2)}'
+ooba
+```
+---
+ contrib/install.sh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/contrib/install.sh b/contrib/install.sh
+index f6a7ccf..cb8a43b 100755
+--- a/contrib/install.sh
++++ b/contrib/install.sh
+@@ -20,7 +20,7 @@ for SRC in $ARGS; do
+ 
+     # If there are surrounding quotes, remove them.  We do this simply by knowing that the destination is always an absolute path
+     if [ "$(echo $DESTFILE | head -c1)" != "/" ]; then
+-        DESTFILE=$(echo $DESTFILE | awk '{print substr($0, 2, length-2)}')
++        DESTFILE=$(echo $DESTFILE | awk '{print substr($0, 2, length($0)-2)}')
+     fi
+ 
+     # Do the chmod dance, and ignore errors on platforms that don't like setting permissions of symlinks
diff --git a/testing/julia/0007-fix-stack-addr.patch b/testing/julia/0007-fix-stack-addr.patch
new file mode 100644
index 0000000000..e627572605
--- /dev/null
+++ b/testing/julia/0007-fix-stack-addr.patch
@@ -0,0 +1,64 @@
+From: Jakub Jirutka <jakub@jirutka.cz>
+Date: Wed, 8 Jun 2016 01:51:00 +0200
+Subject: [PATCH] Try not to use address of local variable as stack address to copy.
+
+It triggers bounds check on musl libc that leads to Illegal instruction error.
+
+This patch is backported from https://github.com/JuliaLang/julia/pull/16813
+--- a/src/gc.c
++++ b/src/gc.c
+@@ -270,10 +270,7 @@
+ 
+ NOINLINE static uintptr_t gc_get_stack_ptr()
+ {
+-    void *dummy = NULL;
+-    // The mask is to suppress the compiler warning about returning
+-    // address of local variable
+-    return (uintptr_t)&dummy & ~(uintptr_t)15;
++    return (uintptr_t)jl_get_frame_addr();
+ }
+ 
+ #include "gc-debug.c"
+--- a/src/julia_internal.h
++++ b/src/julia_internal.h
+@@ -222,6 +222,18 @@
+ 
+ DLLEXPORT jl_value_t *(jl_array_data_owner)(jl_array_t *a);
+ 
++STATIC_INLINE void *jl_get_frame_addr(void)
++{
++#ifdef __GNUC__
++    return __builtin_frame_address(0);
++#else
++    void *dummy = NULL;
++    // The mask is to suppress the compiler warning about returning
++    // address of local variable
++    return (void*)((uintptr_t)&dummy & ~(uintptr_t)15);
++#endif
++}
++
+ #ifdef __cplusplus
+ }
+ #endif
+--- a/src/task.c
++++ b/src/task.c
+@@ -163,8 +163,8 @@
+ {
+     if (t->state == done_sym || t->state == failed_sym)
+         return;
+-    volatile char *_x;
+-    size_t nb = (char*)jl_stackbase - (char*)&_x;
++    char *frame_addr = (char*)jl_get_frame_addr();
++    size_t nb = (char*)jl_stackbase - frame_addr;
+     char *buf;
+     if (t->stkbuf == NULL || t->bufsz < nb) {
+         buf = (char*)allocb(nb);
+@@ -175,7 +175,7 @@
+         buf = (char*)t->stkbuf;
+     }
+     t->ssize = nb;
+-    memcpy(buf, (char*)&_x, nb);
++    memcpy(buf, frame_addr, nb);
+     // this task's stack could have been modified after
+     // it was marked by an incremental collection
+     // move the barrier back instead of walking it again here
diff --git a/testing/julia/0008-ldconfig-compat.patch b/testing/julia/0008-ldconfig-compat.patch
new file mode 100644
index 0000000000..b8a4efaab3
--- /dev/null
+++ b/testing/julia/0008-ldconfig-compat.patch
@@ -0,0 +1,24 @@
+From: Jakub Jirutka <jakub@jirutka.cz>
+Date: Thu, 9 Jun 2016 01:15:00 +0200
+Subject: [PATCH] Use our find-syslibs script instead of /sbin/ldconfig -p
+
+Julia uses "ldconfig -p" to find system libraries. The problem is that musl's
+ldconfig doesn't support the option "-p". Moreover, ldconfig relies on .pc
+files that are installed only with -dev subpackages.
+
+This workaround lies in using custom script that adapts output of scanelf to
+the format produced by "ldconfig -p".
+
+See https://github.com/JuliaLang/julia/issues/6742.
+
+--- a/src/ccall.cpp
++++ b/src/ccall.cpp
+@@ -14,7 +14,7 @@
+     char *line=NULL;
+     size_t sz=0;
+ #if defined(__linux__)
+-    FILE *ldc = popen("/sbin/ldconfig -p", "r");
++    FILE *ldc = popen("/usr/share/julia/find-syslibs", "r");
+ #else
+     FILE *ldc = popen("/sbin/ldconfig -r", "r");
+ #endif
diff --git a/testing/julia/APKBUILD b/testing/julia/APKBUILD
new file mode 100644
index 0000000000..322dbb4b57
--- /dev/null
+++ b/testing/julia/APKBUILD
@@ -0,0 +1,187 @@
+# Contributor: Jakub Jirutka <jakub@jirutka.cz>
+# Maintainer: Jakub Jirutka <jakub@jirutka.cz>
+pkgname=julia
+pkgver=0.4.5
+# Keep in sync with deps/libuv.version.
+_libuv_ver=efb40768b7c7bd9f173a7868f74b92b1c5a61a0e
+# Keep in sync with deps/Versions.make.
+_rmathjulia_ver=0.1
+pkgrel=0
+pkgdesc="A high-level, high-performance dynamic language for technical computing"
+url="http://julialang.org"
+arch="x86 x86_64"
+license="MIT"
+depends="arpack
+	fftw>=3.3
+	gmp>=5.0
+	libgit2>=0.21
+	mpfr3
+	openblas
+	openlibm
+	openspecfun>=0.4
+	pcre2>=10.0
+	suitesparse>=4.1
+	"
+depends_dev="arpack-dev
+	dsfmt-dev
+	fftw-dev
+	gmp-dev
+	libgit2-dev
+	libunwind-dev
+	llvm-dev>=3.7
+	mpfr-dev
+	openblas-dev
+	openlibm-dev
+	openspecfun-dev
+	pcre2-dev
+	suitesparse-dev
+	utf8proc-dev>=1.3
+	"
+makedepends="$depends_dev
+	bash
+	cmake
+	dsfmt
+	gfortran
+	linux-headers
+	openssl-dev
+	paxmark
+	perl
+	"
+subpackages="$pkgname-dev $pkgname-doc $pkgname-debug"
+source="https://github.com/JuliaLang/julia/releases/download/v$pkgver/$pkgname-$pkgver.tar.gz
+	libuv-$_libuv_ver.tar.gz::https://api.github.com/repos/JuliaLang/libuv/tarball/$_libuv_ver
+	Rmath-julia-$_rmathjulia_ver.tar.gz::https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v$_rmathjulia_ver
+	find-syslibs
+	0001-hardened.patch
+	0002-verbose-build.patch
+	0003-no-clean-docs.patch
+	0004-remove-sysctl.h.patch
+	0005-llvm-3.8.patch
+	0006-fix-contrib-install.patch
+	0007-fix-stack-addr.patch
+	0008-ldconfig-compat.patch
+	"
+builddir="$srcdir/$pkgname-$pkgver"
+ldpath="/usr/lib/julia"
+
+prepare() {
+	cd "$builddir"
+
+	cp "$srcdir"/Rmath-julia-$_rmathjulia_ver.tar.gz deps/ || return 1
+
+	# Julia needs patched libuv.
+	cp "$srcdir"/libuv-$_libuv_ver.tar.gz deps/ || return 1
+
+	# Prevent fetching of bundled stuff in the build and package phase.
+	cat <<-EOF > deps/jldownload
+		#!/bin/sh
+		echo "!!! Downloading disabled !!!"
+		echo "Abuild should not fetch any files in the build phase."
+		echo "Add all the needed files to the APKBUILD's source=."
+		exit 1
+	EOF
+
+	cat <<-EOF > Make.user
+		prefix=/usr
+		libexecdir=/usr/lib
+		sysconfdir=/etc
+		DESTDIR="$pkgdir"
+		LIBBLAS=-lopenblas
+		LIBBLASNAME=libopenblas
+		LIBLAPACK=-lopenblas
+		LIBLAPACKNAME=libopenblas
+		USE_SYSTEM_LLVM=1
+		USE_SYSTEM_LIBUNWIND=1
+		USE_SYSTEM_PCRE=1
+		USE_SYSTEM_LIBM=1
+		USE_SYSTEM_OPENLIBM=1
+		USE_SYSTEM_OPENSPECFUN=1
+		USE_SYSTEM_DSFMT=1
+		USE_SYSTEM_BLAS=1
+		USE_SYSTEM_LAPACK=1
+		USE_SYSTEM_FFTW=1
+		USE_SYSTEM_GMP=1
+		USE_SYSTEM_MPFR=1
+		USE_SYSTEM_ARPACK=1
+		USE_SYSTEM_SUITESPARSE=1
+		USE_SYSTEM_LIBUV=0
+		USE_SYSTEM_UTF8PROC=1
+		USE_SYSTEM_LIBGIT2=1
+		USE_SYSTEM_PATCHELF=1
+		USE_LLVM_SHLIB=1
+		VERBOSE=1
+	EOF
+
+	# Pre-SSE2 CPU targets are not supported;
+	# create a generic 32-bit x86 binary.
+	if [ "$CARCH" = x86 ]; then
+		echo "MARCH=i686" >> Make.user
+		echo "JULIA_CPU_TARGET=pentium4" >> Make.user
+	else
+		echo "MARCH=${CARCH/_/-}" >> Make.user
+	fi
+ 
+	default_prepare
+}
+
+build() {
+	cd "$builddir"
+
+	# If we don't clean here, then make install will recompile everything,
+	# don't know why...
+	make clean && make release
+}
+
+package() {
+	cd "$builddir"
+
+	make install || return 1
+	install -D "$srcdir"/find-syslibs "$pkgdir"/usr/share/julia/find-syslibs
+}
+
+debug() {
+	pkgdesc="$pkgdesc (debug build)"
+
+	install -d "$subpkgdir"/usr/bin
+	mv "$pkgdir"/usr/bin/*-debug "$subpkgdir"/usr/bin/ || return 1
+
+	install -d "$subpkgdir"/usr/lib/julia
+	mv "$pkgdir"/usr/lib/julia/*-debug.* "$subpkgdir"/usr/lib/julia/
+}
+
+md5sums="dc2ff07bb6fd5eeae12c7ec41ec38f22  julia-0.4.5.tar.gz
+b94c9164471d0492dce170961d7c65a2  libuv-efb40768b7c7bd9f173a7868f74b92b1c5a61a0e.tar.gz
+4e3f9e41e7b8cd3070225d1f5e8b21d9  Rmath-julia-0.1.tar.gz
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+8a2ced6314457d47739deef08adb9ff4  0001-hardened.patch
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+0fc44cc7b6a0167ee1e36310364e7049  0003-no-clean-docs.patch
+e5a50262e22a97d7f8108e6e8fc160d1  0004-remove-sysctl.h.patch
+aa0a5c577ccd3d0c652d15b6a064594e  0005-llvm-3.8.patch
+ab0e26d5ac79161d7e65481700cf9114  0006-fix-contrib-install.patch
+16f15ab47f1aff789966c90887916e9e  0007-fix-stack-addr.patch
+3cf5ef31fd586ffac9a29cc3eca00e8a  0008-ldconfig-compat.patch"
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+7895279378e08f394501af568b08fb59244c272735045b077de1d7ff67810787  0008-ldconfig-compat.patch"
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diff --git a/testing/julia/find-syslibs b/testing/julia/find-syslibs
new file mode 100755
index 0000000000..ef25263607
--- /dev/null
+++ b/testing/julia/find-syslibs
@@ -0,0 +1,19 @@
+#!/bin/sh
+#
+# This script adapts output of scanelf to the format produced by
+# GNU's "ldconfig -p".
+#
+# Note: Julia uses "ldconfig -p" as a workaround to find system
+# libraries, see https://github.com/JuliaLang/julia/issues/6742.
+#
+set -e
+
+echo 'libs found on ldpath'
+scanelf --ldpath -E ET_DYN -BF '%F %M %S %f' | while read path class soname _; do
+	case "$class" in
+		ELFCLASS32) arch='i686';;
+		ELFCLASS64) arch='x86-64';;
+		*) arch="$(uname -m | sed 's/_/-/g')";;
+	esac
+	printf '\t%s (libc,%s) => %s\n' "$soname" "$arch" "$path"
+done