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community/gap to 4.10.0-4

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This commit is contained in:
Kevin Mihelich 2018-12-23 16:33:57 +00:00
parent 31e73f92ca
commit 2ef458516c
6 changed files with 504 additions and 30 deletions
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49
community/gap/PKGBUILD
View file

@ -8,14 +8,18 @@
pkgbase=gap
pkgname=(gap gap-doc gap-packages)
pkgver=4.10.0
pkgrel=3
pkgrel=4
pkgdesc="Groups, Algorithms, Programming: a system for computational discrete algebra"
arch=(x86_64)
url="https://www.gap-system.org/"
license=(GPL)
source=("https://www.gap-system.org/pub/gap/gap-${pkgver%.*}/tar.gz/gap-$pkgver.tar.gz" gap-no-packages-by-default.patch)
source=("https://www.gap-system.org/pub/gap/gap-${pkgver%.*}/tar.gz/gap-$pkgver.tar.gz" gap.sh
gap-sagemath-1.patch gap-sagemath-2.patch gap-sagemath-3.patch)
sha256sums=('314b8d949c0bb01ef8bee199b29571d42714df660aba0d76ded254f58295904f'
'e8f19968d998172b7c289d0499b8b8a05bc31119a1ce073181d3842ece6fe3a2')
'143fb8a79a52c007903cce13407850df309ef803a9b00398d05169355917de46'
'e5f0a71ae5cdcc6596330834ef9fb0a0183890a9cf874a7eb88b819b0030a33b'
'3b66e6b320f56119b1d8eb804a94ee3a7ea71af10bd4f99a61bae32840e62c87'
'511414a8d085a9ef9de5f921fdd45e4bbb3f33c2d88b821da06dfc267c182ddc')
makedepends=(libxaw givaro mpfi normaliz boost c-xsc zeromq fplll polymake wget chrpath)
prepare() {
@ -23,10 +27,13 @@ prepare() {
# Use system normaliz
sed -e '/build-normaliz.sh/d' -i bin/BuildPackages.sh
# Don't load any packages by default
patch -p1 -i ../gap-no-packages-by-default.patch
# Disable anupq package, it's i686 only
rm -r pkg/anupq-*
# Patches to make sagemath work with GAP's libgap
patch -p1 -i ../gap-sagemath-1.patch
patch -p1 -i ../gap-sagemath-2.patch
patch -p1 -i ../gap-sagemath-3.patch
}
build() {
@ -39,28 +46,33 @@ build() {
../bin/BuildPackages.sh
}
_standardpkgs=(GAPDoc-* primgrp-* SmallGrp-* transgrp atlasrep autpgrp-* alnuth-* crisp-* ctbllib FactInt-* fga irredsol-* laguna-*
polenta-* polycyclic-* resclasses-* sophus-* tomlib-*)
package_gap() {
depends=(gmp)
depends=(gmp zlib)
optdepends=('gap-packages: extra packages' 'gap-doc: documentation')
# conflicts=(libgap)
replaces=(gap-data)
conflicts=(libgap)
replaces=(gap-data libgap gap-4.8 gap-4.8-data)
cd gap-$pkgver
# make DESTDIR="$pkgdir" install
make DESTDIR="$pkgdir" install-headers install-libgap
# Install missing header
install -Dm644 gen/config.h -t "$pkgdir"/usr/include/gap
mkdir -p "$pkgdir"/usr/{bin,lib/gap/pkg}
cp -r grp lib "$pkgdir"/usr/lib/gap
cp -r pkg/{GAPDoc-*,primgrp-*,SmallGrp-*,transgrp} "$pkgdir"/usr/lib/gap/pkg
install -m755 gap -t "$pkgdir"/usr/lib/gap
sed -e "s|/build/gap/src/gap-$pkgver|/usr/lib/gap|g" bin/gap.sh > "$pkgdir"/usr/bin/gap
chmod 755 "$pkgdir"/usr/bin/gap
# install missing header
# cp gen/config.h "$pkgdir"/usr/include/gap
for _pkg in ${_standardpkgs[@]}; do
cp -r pkg/$_pkg "$pkgdir"/usr/lib/gap/pkg
done
install -Dm755 gap -t "$pkgdir"/usr/lib/gap
# Install launcher script
install -Dm755 "$srcdir"/gap.sh "$pkgdir"/usr/bin/gap
}
package_gap-doc() {
depends=(gap)
replaces=(gap-4.8-doc)
pkgdesc="Documentation for GAP"
cd gap-$pkgver
@ -70,6 +82,7 @@ package_gap-doc() {
package_gap-packages() {
depends=(gap)
replaces=(gap-4.8-packages)
optdepends=('normaliz: Normaliz interface package' 'libxaw: xgap package' 'c-xsc: float package' 'mpfi: float package'
'libmpc: float package' 'fplll: float package' 'zeromq: ZeroMQ interface package'
'polymake: Polymake interface package' 'curl: curl interface package')
@ -80,7 +93,9 @@ package_gap-packages() {
cp -r pkg "$pkgdir"/usr/lib/gap
# provided by main gap package
rm -r "$pkgdir"/usr/lib/gap/pkg/{GAPDoc-*,primgrp-*,SmallGrp-*,transgrp}
for _pkg in ${_standardpkgs[@]}; do
rm -r "$pkgdir"/usr/lib/gap/pkg/$_pkg
done
# fix RPATH
if [[ $CARCH == "aarch64" ]]; then

13
community/gap/gap-no-packages-by-default.patch
View file

@ -1,13 +0,0 @@
--- gap4r8/lib/package.gi.orig 2016-11-25 18:59:02.234113245 +0000
+++ gap4r8/lib/package.gi 2016-11-25 18:59:53.093996139 +0000
@@ -1743,9 +1743,7 @@
For backwards compatibility, the default lists most of packages \
that were autoloaded in GAP 4.4 (add or remove packages as you like)."
],
- default:= [ "autpgrp", "alnuth", "crisp", "ctbllib", "factint", "fga",
- "irredsol", "laguna", "polenta", "polycyclic", "resclasses",
- "sophus", "tomlib" ],
+ default:= [ ],
values:= function() return RecNames( GAPInfo.PackagesInfo ); end,
multi:= true,
) );

74
community/gap/gap-sagemath-1.patch Normal file
View file

@ -0,0 +1,74 @@
From 163b8aae99b1b206e5ae85763e21f47b7651f9c4 Mon Sep 17 00:00:00 2001
From: "Erik M. Bray" <erik.bray@lri.fr>
Date: Tue, 4 Dec 2018 12:44:23 +0000
Subject: [PATCH 1/3] a version of the writeandcheck.patch from Sage that works
against 4.10
---
src/sysfiles.c | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/src/sysfiles.c b/src/sysfiles.c
index 2250784..45b4347 100644
--- a/src/sysfiles.c
+++ b/src/sysfiles.c
@@ -159,21 +159,23 @@ SYS_SY_BUFFER syBuffers[32];
/* utility to check return value of 'write' */
ssize_t echoandcheck(int fid, const char *buf, size_t count) {
int ret;
+ static int depth = 0;
+ depth++;
if (syBuf[fid].type == gzip_socket) {
ret = gzwrite(syBuf[fid].gzfp, buf, count);
- if (ret < 0)
+ if (ret < 0 && depth == 1)
ErrorQuit(
"Could not write to compressed file, see 'LastSystemError();'\n",
0L, 0L);
}
else {
ret = write(syBuf[fid].echo, buf, count);
- if (ret < 0)
+ if (ret < 0 && depth == 1)
ErrorQuit("Could not write to file descriptor %d, see "
"'LastSystemError();'\n",
syBuf[fid].fp, 0L);
}
-
+ depth--;
return ret;
}
@@ -1636,21 +1638,27 @@ Int SyWrite(Int fid, const void * ptr, size_t len)
static ssize_t SyWriteandcheck(Int fid, const void * buf, size_t count)
{
int ret;
+ static int depth = 0;
+ depth++;
if (syBuf[fid].type == gzip_socket) {
ret = gzwrite(syBuf[fid].gzfp, buf, count);
- if (ret < 0)
+ if (ret < 0 && depth == 1) {
ErrorQuit(
"Cannot write to compressed file, see 'LastSystemError();'\n",
0L, 0L);
+ }
}
else {
ret = write(syBuf[fid].fp, buf, count);
- if (ret < 0)
+ if (ret < 0 && depth == 1) {
ErrorQuit("Cannot write to file descriptor %d, see "
"'LastSystemError();'\n",
syBuf[fid].fp, 0L);
+ }
}
+ depth--;
+
return ret;
}
--
1.9.1

122
community/gap/gap-sagemath-2.patch Normal file
View file

@ -0,0 +1,122 @@
From 0cecb79ff97c73a24acacf8afdc3edba93507661 Mon Sep 17 00:00:00 2001
From: "Erik M. Bray" <erik.bray@lri.fr>
Date: Thu, 22 Nov 2018 10:53:31 +0100
Subject: [PATCH 2/3] kernel: add helper function for writing error messages to
the file/stream referenced by the ERROR_OUTPUT global variable
---
src/error.c | 42 ++++++++++++++++++++++++++++++++++++++++++
src/error.h | 8 ++++++++
src/scanner.c | 3 ++-
3 files changed, 52 insertions(+), 1 deletion(-)
diff --git a/src/error.c b/src/error.c
index 9bb3be8..d43347d 100644
--- a/src/error.c
+++ b/src/error.c
@@ -33,6 +33,8 @@
static Obj ErrorInner;
+static Obj ERROR_OUTPUT = NULL;
+static Obj IsOutputStream;
/****************************************************************************
@@ -40,6 +42,44 @@ static Obj ErrorInner;
*F * * * * * * * * * * * * * * error functions * * * * * * * * * * * * * * *
*/
+/****************************************************************************
+**
+*F OpenErrorOutput() . . . . . . . open the file or stream assigned to the
+** ERROR_OUTPUT global variable defined in
+** error.g, or "*errout*" otherwise
+*/
+UInt OpenErrorOutput( void )
+{
+ /* Try to print the output to stream. Use *errout* as a fallback. */
+ UInt ret = 0;
+
+ if (ERROR_OUTPUT != NULL) {
+ if (IsStringConv(ERROR_OUTPUT)) {
+ ret = OpenOutput(CSTR_STRING(ERROR_OUTPUT));
+ }
+ else {
+ if (CALL_1ARGS(IsOutputStream, ERROR_OUTPUT) == True) {
+ ret = OpenOutputStream(ERROR_OUTPUT);
+ }
+ }
+ }
+
+ if (!ret) {
+ /* It may be we already tried and failed to open *errout* above but
+ * but this is an extreme case so it can't hurt to try again
+ * anyways */
+ ret = OpenOutput("*errout*");
+ if (ret) {
+ Pr("failed to open error stream\n", 0, 0);
+ }
+ else {
+ Panic("failed to open *errout*");
+ }
+ }
+
+ return ret;
+}
+
/****************************************************************************
**
@@ -615,6 +655,8 @@ static Int InitKernel(StructInitInfo * module)
InitHdlrFuncsFromTable(GVarFuncs);
ImportFuncFromLibrary("ErrorInner", &ErrorInner);
+ ImportFuncFromLibrary("IsOutputStream", &IsOutputStream);
+ ImportGVarFromLibrary("ERROR_OUTPUT", &ERROR_OUTPUT);
// return success
return 0;
diff --git a/src/error.h b/src/error.h
index 31af256..1f5ee5d 100644
--- a/src/error.h
+++ b/src/error.h
@@ -32,6 +32,14 @@ Int RegisterBreakloopObserver(intfunc func);
/****************************************************************************
**
+*F OpenErrorOutput() . . . . . . . open the file or stream assigned to the
+** ERROR_OUTPUT global variable defined in
+** error.g, or "*errout*" otherwise
+*/
+extern UInt OpenErrorOutput();
+
+/****************************************************************************
+**
*F ErrorQuit( <msg>, <arg1>, <arg2> ) . . . . . . . . . . . print and quit
*/
extern void ErrorQuit(const Char * msg, Int arg1, Int arg2) NORETURN;
diff --git a/src/scanner.c b/src/scanner.c
index 4db17b3..071c0e3 100644
--- a/src/scanner.c
+++ b/src/scanner.c
@@ -16,6 +16,7 @@
#include "scanner.h"
+#include "error.h"
#include "gapstate.h"
#include "gaputils.h"
#include "io.h"
@@ -42,7 +43,7 @@ static void SyntaxErrorOrWarning(const Char * msg, UInt error)
if (STATE(NrErrLine) == 0) {
// open error output
- OpenOutput("*errout*");
+ OpenErrorOutput();
// print the message ...
if (error)
--
1.9.1

269
community/gap/gap-sagemath-3.patch Normal file
View file

@ -0,0 +1,269 @@
From 798756448180195a6ce020565a5c1d160e491e98 Mon Sep 17 00:00:00 2001
From: "Erik M. Bray" <erik.bray@lri.fr>
Date: Thu, 6 Dec 2018 16:11:35 +0000
Subject: [PATCH 3/3] Prototype for GAP_Enter/Leave macros to bracket use of
libgap and stack local GAP objects in code which embeds libgap
There are two parts to this:
First, the outer-most GAP_Enter() must set the StackBottom variable for GASMAN,
without which objects tracked by GASMAN that are allocated on the stack are
properly tracked (see #3089).
Second, the outer-most GAP_Enter() call should set a jump point for longjmps to
STATE(ReadJmpError). Code within the GAP kernel may reset this, but we should
set it here in case any unexpected errors occur within the GAP kernel that are
not already handled appropriately by a TRY_IF_NO_ERROR.
For the first issue, we add GAP_EnterStack() and GAP_LeaveStack() macros which
implement *just* the StackBottom handling without any other error handling. We
also add a function to gasman.c called _MarkStackBottomBags which just updates
the StackBottom variable. Then the macro called MarkStackBottomBags (same name
without underscore) can be used within a function to set StackBottom to
somewhere at or near the beginning of that function's stack frame. This uses
GCC's __builtin_frame_address, but supported is probably needed for other
platforms that don't have this.
The state variable STATE(EnterStackCount) is used to track recursive calls into
GAP_EnterStack(). We only want to set StackBottom on the outer-most call. The
count is decremented on GAP_LeaveStack(). Some functions are provided for
manipulating the counter from the API without directly exposing the GAP state,
but I'm not sure if this is necessary or desirable, especially since it means
EnterStackCount isn't updated atomically. My hope was to avoid exposing too
many GAP internals, but it may be necessary in order to implement these as
macros.
For setting the STATE(ReadJmpError) jump buffer we provide a macro called
GAP_Error_Setjmp() which is fairly straightforward, except that it needs to be
written in such a way that it can be used in concert correctly with
GAP_EnterStack(). In particular, if returning to the site of a
GAP_Error_Setjmp() call we do not want to accidentally re-increment the
EnterStackCount.
Finally, the higher-level GAP_Enter() and GAP_Leave() macros are provided: The
latter is just an alias for GAP_LeaveStack(), but the former carefully combines
*both* GAP_Error_Setjmp() and GAP_EnterStack(). Although called like a
function, the GAP_Enter() macro expands to a compound statement (necessary for
both GAP_EnterStack() and GAP_Error_Setjmp() to work properly). The order of
expansion is also deliberate so that this can be used like:
jmp_retval = GAP_Enter();
so that the return value of the setjmp call can be stored in a variable while
using GAP_Enter(), and can be checked to see whether an error occurred.
However, this requires some care to ensure that the following GAP_EnterStack()
doesn't increment the EnterStackCount following a return to this point via a
longjmp.
Conflicts:
src/libgap-api.h
---
src/gapstate.h | 3 ++
src/gasman.c | 6 ++++
src/gasman.h | 15 ++++++++++
src/libgap-api.c | 27 +++++++++++++++++
src/libgap-api.h | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--
5 files changed, 137 insertions(+), 2 deletions(-)
diff --git a/src/gapstate.h b/src/gapstate.h
index 72ec4c3..7a2a663 100644
--- a/src/gapstate.h
+++ b/src/gapstate.h
@@ -97,6 +97,9 @@ typedef struct GAPState {
UInt1 StateSlots[STATE_SLOTS_SIZE];
+ /* For libgap-api.c */
+ Int EnterStackCount;
+
/* Allocation */
#if !defined(USE_GASMAN)
#define MAX_GC_PREFIX_DESC 4
diff --git a/src/gasman.c b/src/gasman.c
index 13c0b1e..4d2ab3d 100644
--- a/src/gasman.c
+++ b/src/gasman.c
@@ -1193,6 +1193,12 @@ void SetExtraMarkFuncBags(TNumExtraMarkFuncBags func)
}
+
+void _MarkStackBottomBags(void* StackBottom) {
+ StackBottomBags = StackBottom;
+}
+
+
void InitBags (
UInt initial_size,
Bag * stack_bottom,
diff --git a/src/gasman.h b/src/gasman.h
index 236eb8b..55e057a 100644
--- a/src/gasman.h
+++ b/src/gasman.h
@@ -982,6 +982,21 @@ extern void InitCollectFuncBags (
typedef void (*TNumExtraMarkFuncBags)(void);
extern void SetExtraMarkFuncBags(TNumExtraMarkFuncBags func);
+
+#ifdef __GNUC__
+#define MarkStackBottomBags() \
+ _MarkStackBottomBags(__builtin_frame_address(0));
+/*
+#else
+ * TODO: Detect the best stack frame detection technique at configure time
+ *
+#define MarkStackBottomBags() \
+ register void* rbp asm("rbp"); \
+ _MarkStackBottomBags(rbp);
+*/
+#endif
+extern void _MarkStackBottomBags(void* StackBottom);
+
/****************************************************************************
**
*F InitBags(...) . . . . . . . . . . . . . . . . . . . . . initialize Gasman
diff --git a/src/libgap-api.c b/src/libgap-api.c
index 82cc441..e75b0e2 100644
--- a/src/libgap-api.c
+++ b/src/libgap-api.c
@@ -10,6 +10,8 @@
#include "lists.h"
#include "streams.h"
#include "stringobj.h"
+#include "system.h"
+
//
// Setup and initialisation
@@ -60,3 +62,28 @@ Obj GAP_EvalString(const char * cmd)
res = READ_ALL_COMMANDS(instream, False, True, viewObjFunc);
return res;
}
+
+inline syJmp_buf * _GAP_GetReadJmpError(void)
+{
+ return &(STATE(ReadJmpError));
+}
+
+inline Int _GAP_GetEnterStackCount(void)
+{
+ return STATE(EnterStackCount);
+}
+
+inline void _GAP_IncEnterStackCount(void)
+{
+ STATE(EnterStackCount)++;
+}
+
+inline void _GAP_DecEnterStackCount(void)
+{
+ STATE(EnterStackCount)--;
+}
+
+inline void _GAP_SetEnterStackCount(Int count)
+{
+ STATE(EnterStackCount) = count;
+}
diff --git a/src/libgap-api.h b/src/libgap-api.h
index e45d6fc..55fcd05 100644
--- a/src/libgap-api.h
+++ b/src/libgap-api.h
@@ -5,9 +5,93 @@
#include "gap.h"
-typedef void (*CallbackFunc)(void);
+#ifdef __GNUC__
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else
+#define unlikely(x) (x)
+#endif
+
+
+#ifndef GAP_ENTER_DEBUG
+#define GAP_ENTER_DEBUG 0
+#endif
+
+
+extern syJmp_buf * _GAP_GetReadJmpError(void);
+extern Int _GAP_GetEnterStackCount(void);
+extern void _GAP_IncEnterStackCount(void);
+extern void _GAP_DecEnterStackCount(void);
+extern void _GAP_SetEnterStackCount(Int count);
+
+
+#if GAP_ENTER_DEBUG
+#define GAP_ENTER_DEBUG_MESSAGE(message, file, line) \
+ fprintf(stderr, "%s: %d; %s:%d\n", message, _GAP_EnterStackCount, file, line);
+#else
+#define GAP_ENTER_DEBUG_MESSAGE(message, file, line)
+#endif
+
+
+#define GAP_EnterStack() \
+ GAP_ENTER_DEBUG_MESSAGE("EnterStack", __FILE__, __LINE__); \
+ Int _gap_tmp_enter_stack_count = _GAP_GetEnterStackCount(); \
+ if (_gap_tmp_enter_stack_count < 0) { \
+ _GAP_SetEnterStackCount(-_gap_tmp_enter_stack_count); \
+ } else { \
+ if (_gap_tmp_enter_stack_count == 0) { \
+ MarkStackBottomBags(); \
+ } \
+ _GAP_IncEnterStackCount(); \
+ }
+
-// Initialisation and finalization
+#define GAP_LeaveStack() \
+ _GAP_DecEnterStackCount(); \
+ GAP_ENTER_DEBUG_MESSAGE("LeaveStack", __FILE__, __LINE__);
+
+
+static inline int _GAP_Error_Prejmp(const char* file, int line) {
+#if GAP_ENTER_DEBUG
+ GAP_ENTER_DEBUG_MESSAGE("Error_Prejmp", file, line);
+#endif
+ if (_GAP_GetEnterStackCount() > 0) {
+ return 1;
+ }
+ return 0;
+}
+
+
+static inline int _GAP_Error_Postjmp(int JumpRet)
+{
+ if (unlikely(JumpRet != 0)) {
+ /* This only should have been called from the outer-most
+ * GAP_EnterStack() call so make sure it resets the EnterStackCount; We
+ * set EnterStackCount to its negative which indicates to
+ * GAP_EnterStack that we just returned from a long jump and should
+ * reset EnterStackCount to its value at the return point rather than
+ * increment it again */
+ Int tmp_count = _GAP_GetEnterStackCount();
+ if (tmp_count > 0) {
+ _GAP_SetEnterStackCount(-tmp_count);
+ }
+ return 0;
+ }
+
+ return 1;
+}
+
+#define GAP_Error_Setjmp() (_GAP_Error_Prejmp(__FILE__, __LINE__) || \
+ _GAP_Error_Postjmp(sySetjmp(*_GAP_GetReadJmpError())))
+
+
+#define GAP_Enter() GAP_Error_Setjmp(); GAP_EnterStack()
+#define GAP_Leave() GAP_LeaveStack()
+
+
+////
+//// Setup and initialisation
+////
+typedef void (*CallbackFunc)(void);
void GAP_Initialize(int argc,
char ** argv,
--
1.9.1

7
community/gap/gap.sh Normal file
View file

@ -0,0 +1,7 @@
#!/bin/sh
GAP_ROOT="/usr/lib/gap"
GAP_DIR=$GAP_ROOT
GAP_EXE=$GAP_ROOT
exec "$GAP_EXE/gap" -l "$GAP_DIR" "$@"