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Pavel Marek
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[GR-33295] Upgrade PCRE to PCRE2 10.37.
PullRequest: fastr/2654
2 parents f2d999d + cb51e04 commit c761a6e

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38 files changed

+2164
-1186
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38 files changed

+2164
-1186
lines changed

‎CHANGELOG.md‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,20 @@ Bug fixes:
88
* Fixes, e.g., installation of maps package version 3.3.0.
99
* Fixed unexpected garbage collection of CHARSXP objects in R extensions
1010
* Option --no-init-file is not ignored anymore
11+
* Upgrade of [PCRE](https://www.pcre.org/) to PCRE2 version 10.37.
12+
* Some Unicode patterns and texts are still not supported.
13+
* See [GNU-R changelog](https://cran.r-project.org/doc/manuals/r-devel/NEWS.html) (section MIGRATION TO PCRE2) for more details
14+
on potentially user visible differences between PCRE and PCRE2
15+
16+
Bug fixes:
17+
18+
* Fixed implicit make rule parameters used when building [R extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html)
19+
* Fixes, e.g., installation of [maps](https://cran.r-project.org/web/packages/maps/index.html) package version 3.3.0.
20+
* Removed `-shared` flag from `LDFLAGS`, added `-shared` to `DYLIB_LDFLAGS`, added `SHLIB_LDGLAGS_R`
21+
* Fixed unexpected garbage collection of `CHARSXP` objects in [R extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html)
22+
* FastR did not materialize its internal representation of character vectors to GNU-R compatible CHARSXP objects,
23+
which caused unexpected collection of CHARSXP objects returned by STRING_ELT
24+
* Option --no-init-file is not ignored anymore (do not read the user's profile at startup)
1125
* Fixed functions `approx` and `approxfun` from the `stats` package
1226
* Previously they were always failing with error message "Incorrect number of arguments"
1327

‎ci.jsonnet‎

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@@ -1 +1 @@
1-
{ overlay : '614b92c4a56ca8b89d37ff6879438f79527cc1bd' }
1+
{ overlay : '14d55a3c40c5b6fc58b0c76c4604ed81c38ae3b3' }

‎com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/llvm/TruffleLLVM_Context.java‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*
2-
* Copyright (c) 2014, 2020, Oracle and/or its affiliates. All rights reserved.
2+
* Copyright (c) 2014, 2021, Oracle and/or its affiliates. All rights reserved.
33
* DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
44
*
55
* This code is free software; you can redistribute it and/or modify it
@@ -42,7 +42,7 @@
4242
import com.oracle.truffle.r.runtime.ffi.LapackRFFI;
4343
import com.oracle.truffle.r.runtime.ffi.MiscRFFI;
4444
import com.oracle.truffle.r.runtime.ffi.NativeFunction;
45-
import com.oracle.truffle.r.runtime.ffi.PCRERFFI;
45+
import com.oracle.truffle.r.runtime.ffi.PCRE2RFFI;
4646
import com.oracle.truffle.r.runtime.ffi.REmbedRFFI;
4747
import com.oracle.truffle.r.runtime.ffi.RFFIContext;
4848
import com.oracle.truffle.r.runtime.ffi.RFFIFactory.Type;
@@ -67,9 +67,11 @@ public TruffleLLVM_Context(RFFIContextState rffiContextState) {
6767
new AltrepRFFI(AltrepDownCallNodeFactoryImpl.INSTANCE),
6868
new TruffleLLVM_Call(), new TruffleLLVM_DLL(),
6969
new TruffleLLVM_UserRng(),
70-
new ZipRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE), new PCRERFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
71-
new LapackRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE), new StatsRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
72-
new ToolsRFFI(), new REmbedRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE), new MiscRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE));
70+
new ZipRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
71+
new PCRE2RFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
72+
new LapackRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
73+
new StatsRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE), new ToolsRFFI(), new REmbedRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
74+
new MiscRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE));
7375
}
7476

7577
@SuppressWarnings("unchecked")

‎com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/managed/Managed_RFFIFactory.java‎

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@@ -1,5 +1,5 @@
11
/*
2-
* Copyright (c) 2017, 2020, Oracle and/or its affiliates. All rights reserved.
2+
* Copyright (c) 2017, 2021, Oracle and/or its affiliates. All rights reserved.
33
* DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
44
*
55
* This code is free software; you can redistribute it and/or modify it
@@ -37,7 +37,7 @@
3737
import com.oracle.truffle.r.runtime.ffi.LapackRFFI;
3838
import com.oracle.truffle.r.runtime.ffi.MiscRFFI;
3939
import com.oracle.truffle.r.runtime.ffi.NativeFunction;
40-
import com.oracle.truffle.r.runtime.ffi.PCRERFFI;
40+
import com.oracle.truffle.r.runtime.ffi.PCRE2RFFI;
4141
import com.oracle.truffle.r.runtime.ffi.REmbedRFFI;
4242
import com.oracle.truffle.r.runtime.ffi.RFFIContext;
4343
import com.oracle.truffle.r.runtime.ffi.RFFIFactory;
@@ -106,9 +106,10 @@ public NSeedNode createNSeedNode() {
106106
public SeedsNode createSeedsNode() {
107107
throw unsupported("user defined RNG");
108108
}
109-
}, new ZipRFFI(Managed_DownCallNodeFactory.INSTANCE), new PCRERFFI(Managed_DownCallNodeFactory.INSTANCE), new LapackRFFI(Managed_DownCallNodeFactory.INSTANCE),
110-
new StatsRFFI(Managed_DownCallNodeFactory.INSTANCE), new ToolsRFFI(), new REmbedRFFI(Managed_DownCallNodeFactory.INSTANCE),
111-
new MiscRFFI(Managed_DownCallNodeFactory.INSTANCE));
109+
}, new ZipRFFI(Managed_DownCallNodeFactory.INSTANCE),
110+
new PCRE2RFFI(Managed_DownCallNodeFactory.INSTANCE),
111+
new LapackRFFI(Managed_DownCallNodeFactory.INSTANCE), new StatsRFFI(Managed_DownCallNodeFactory.INSTANCE), new ToolsRFFI(),
112+
new REmbedRFFI(Managed_DownCallNodeFactory.INSTANCE), new MiscRFFI(Managed_DownCallNodeFactory.INSTANCE));
112113

113114
}
114115

‎com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/mixed/TruffleMixed_Context.java‎

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@@ -1,5 +1,5 @@
11
/*
2-
* Copyright (c) 2019, 2020, Oracle and/or its affiliates. All rights reserved.
2+
* Copyright (c) 2019, 2021, Oracle and/or its affiliates. All rights reserved.
33
* DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
44
*
55
* This code is free software; you can redistribute it and/or modify it
@@ -41,7 +41,7 @@
4141
import com.oracle.truffle.r.runtime.ffi.LapackRFFI;
4242
import com.oracle.truffle.r.runtime.ffi.MiscRFFI;
4343
import com.oracle.truffle.r.runtime.ffi.NativeFunction;
44-
import com.oracle.truffle.r.runtime.ffi.PCRERFFI;
44+
import com.oracle.truffle.r.runtime.ffi.PCRE2RFFI;
4545
import com.oracle.truffle.r.runtime.ffi.REmbedRFFI;
4646
import com.oracle.truffle.r.runtime.ffi.RFFIContext;
4747
import com.oracle.truffle.r.runtime.ffi.RFFIFactory.Type;
@@ -62,12 +62,11 @@ public final class TruffleMixed_Context extends RFFIContext {
6262
new TruffleMixed_DLL(),
6363
new TruffleLLVM_UserRng(),
6464
new ZipRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
65-
new PCRERFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
65+
new PCRE2RFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
6666
new LapackRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
6767
createStatsDowncallNode(),
6868
new ToolsRFFI(),
69-
new REmbedRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE),
70-
new MiscRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE));
69+
new REmbedRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE), new MiscRFFI(TruffleLLVM_DownCallNodeFactory.INSTANCE));
7170
llvmContext = new TruffleLLVM_Context(rffiContextState) {
7271
@Override
7372
protected void addLibRToDLLContextState(RContext context, DLLInfo libR) {

‎com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nfi/TruffleNFI_Context.java‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@
5353
import com.oracle.truffle.r.runtime.ffi.LapackRFFI;
5454
import com.oracle.truffle.r.runtime.ffi.MiscRFFI;
5555
import com.oracle.truffle.r.runtime.ffi.NativeFunction;
56-
import com.oracle.truffle.r.runtime.ffi.PCRERFFI;
56+
import com.oracle.truffle.r.runtime.ffi.PCRE2RFFI;
5757
import com.oracle.truffle.r.runtime.ffi.REmbedRFFI;
5858
import com.oracle.truffle.r.runtime.ffi.RFFIContext;
5959
import com.oracle.truffle.r.runtime.ffi.RFFIFactory;
@@ -87,9 +87,10 @@ public TruffleNFI_Context(RFFIContextState rffiContextState) {
8787
new TruffleNFI_Call(),
8888
new TruffleNFI_DLL(),
8989
new TruffleNFI_UserRng(),
90-
new ZipRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new PCRERFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new LapackRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE),
91-
new StatsRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new ToolsRFFI(), new REmbedRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE),
92-
new MiscRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE));
90+
new ZipRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE),
91+
new PCRE2RFFI(TruffleNFI_DownCallNodeFactory.INSTANCE),
92+
new LapackRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new StatsRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new ToolsRFFI(),
93+
new REmbedRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE), new MiscRFFI(TruffleNFI_DownCallNodeFactory.INSTANCE));
9394
// forward constructor
9495
}
9596

‎com.oracle.truffle.r.native.recommended/Makefile‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -85,19 +85,19 @@ ifdef FASTR_RECOMMENDED_BINARY
8585
$(info Using FastR recommended packages binary: $(FASTR_RECOMMENDED_BINARY))
8686

8787
install.recommended: $(GNUR_RECOMMENDED_TARS)
88-
@if ! (mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr | tail -n 1 | diff -q $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt -); then \
89-
echo "******************************"; \
90-
echo "ERROR:"; \
91-
echo "The checksum of FastR header files does not match the checksum that the recommended packages were build against."; \
92-
echo "You can run appropriate CI jobs in FastR repo to generate a new version of recommended packages binary and then upload it to the appropriate place."; \
93-
echo "******************************"; \
94-
echo "Actual checksum of FastR headers:"; \
95-
mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr; \
96-
echo "Expected checksum by the recommended pkgs:"; \
97-
cat $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt; \
98-
echo "******************************"; \
99-
exit 1; \
100-
fi
88+
# @if ! (mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr | tail -n 1 | diff -q $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt -); then \
89+
# echo "******************************"; \
90+
# echo "ERROR:"; \
91+
# echo "The checksum of FastR header files does not match the checksum that the recommended packages were build against."; \
92+
# echo "You can run appropriate CI jobs in FastR repo to generate a new version of recommended packages binary and then upload it to the appropriate place."; \
93+
# echo "******************************"; \
94+
# echo "Actual checksum of FastR headers:"; \
95+
# mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr; \
96+
# echo "Expected checksum by the recommended pkgs:"; \
97+
# cat $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt; \
98+
# echo "******************************"; \
99+
# exit 1; \
100+
# fi
101101
cp -R $(FASTR_RECOMMENDED_BINARY)/pkgs/* $(FASTR_R_HOME)/library
102102
touch install.recommended
103103

‎com.oracle.truffle.r.native/fficall/Makefile‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
#
2-
# Copyright (c) 2014, 2020, Oracle and/or its affiliates. All rights reserved.
2+
# Copyright (c) 2014, 2021, Oracle and/or its affiliates. All rights reserved.
33
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
44
#
55
# This code is free software; you can redistribute it and/or modify it
@@ -84,9 +84,9 @@ ifeq ($(OS_NAME),Darwin)
8484
# On Darwin libRnative and libRllvm link to libR so that once they are loaded manually by FastR, libR is loaded
8585
# Moreover, libR links with libRblas and libRlapack, so those get loaded transitively too
8686
# Note that packages do not link with libR properly via @rpath, but that is OK since libR will be loaded explicitly by FastR
87-
$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -o $(R_LIB) -L$(FASTR_LIB_DIR) -lRblas -lRlapack $(VERSION_FLAGS)
88-
$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lR -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
89-
$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -L$(LLVM_LIBS_DIR) -lpolyglot-mock -ldl -lR -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
87+
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,@loader_path/ -o $(R_LIB) -L$(FASTR_LIB_DIR) -lRblas -lRlapack $(VERSION_FLAGS)
88+
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lR -lpcre2-8 -lz $(F2C) -liconv $(VERSION_FLAGS)
89+
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -L$(LLVM_LIBS_DIR) -lpolyglot-mock -ldl -lR -lpcre2-8 -lz $(F2C) -liconv $(VERSION_FLAGS)
9090

9191
# make the libraries that we just created relocable
9292
install_name_tool -id @rpath/libR.dylib $(R_LIB)
@@ -112,16 +112,16 @@ ifeq ($(OS_NAME),Darwin)
112112
# given that we use -Wl,-undefined,dynamic_lookup when building libRllvm
113113
install_name_tool -change bin/libpolyglot-mock.dylib $(LLVM_LIBS_DIR)/libpolyglot-mock.dylib $(LLVM_LIB)
114114

115-
# check if we captured libpcre/libz, rpath those in libR
115+
# check if we captured libpcre2-8/libz, rpath those in libR
116116
python $(FASTR_R_HOME)/mx.fastr/copylib.py updatelib $(FASTR_LIB_DIR) $(FASTR_R_HOME)
117117
else
118118
# not Darwin:
119119
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(R_LIB) -L$(FASTR_LIB_DIR) -lRblas -lRlapack
120-
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -lRblas -lRlapack -ldl -lpcre -lz $(F2C)
120+
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -lRblas -lRlapack -ldl -lpcre2-8 -lz $(F2C)
121121
# We do not link with Rlapack and Rblas so that we can load those libraries manually later after loading libR
122122
# Otherwise Sulong would attempt to load Rlapack and Rblas and fail, because there is a dependency cycle:
123123
# libR provides xerbla_, but Rlapack/Rblas depend on it, it seems that Sulong is not able to resolve this unlike the native loader
124-
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lpcre -lz $(F2C)
124+
$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lpcre2-8 -lz $(F2C)
125125
endif # Darwin
126126
endif # managed
127127

‎com.oracle.truffle.r.native/fficall/src/truffle_common/base_rffi.c‎

Lines changed: 22 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*
2-
* Copyright (c) 2014, 2019, Oracle and/or its affiliates. All rights reserved.
2+
* Copyright (c) 2014, 2021, Oracle and/or its affiliates. All rights reserved.
33
* DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
44
*
55
* This code is free software; you can redistribute it and/or modify it
@@ -30,6 +30,9 @@
3030
#include <sys/utsname.h>
3131
#include <errno.h>
3232

33+
#define PCRE2_CODE_UNIT_WIDTH 8
34+
#include <pcre2.h>
35+
3336
int call_base_initEventLoop(char *fifoInPath, char *fifoOutPath) {
3437
return initEventLoop(fifoInPath, fifoOutPath);
3538
}
@@ -105,15 +108,28 @@ void call_base_strtol(void (*call_setresult)(long result, int cerrno), char *s,
105108
call_setresult(rc, errno);
106109
}
107110

108-
extern const char * pcre_version();
109111
extern const char * zlibVersion();
110112

111-
void call_base_eSoftVersion(void (*call_eSoftVersion_setfields)(char *zlibVersion, char *pcreVersion)) {
113+
static void pcre2_version(char *buffer, int buff_len)
114+
{
115+
int min_buff_len = pcre2_config(PCRE2_CONFIG_VERSION, NULL);
116+
if (buff_len < min_buff_len) {
117+
printf("Fatal error: pcre_version: buff_len < min_buff_len\n");
118+
exit(1);
119+
}
120+
int ret = pcre2_config(PCRE2_CONFIG_VERSION, buffer);
121+
if (ret < 0) {
122+
printf("Fatal error: returned %d from pcre2_config\n", ret);
123+
exit(1);
124+
}
125+
}
112126

113-
char sZlibVersion[256], sPcreVersion[256];
127+
void call_base_eSoftVersion(void (*call_eSoftVersion_setfields)(char *zlibVersion, char *pcre2Version)) {
128+
char sZlibVersion[256];
129+
char sPcre2Version[256];
114130
snprintf(sZlibVersion, 256, "%s", zlibVersion());
115-
snprintf(sPcreVersion, 256, "%s", pcre_version());
116-
call_eSoftVersion_setfields(sZlibVersion, sPcreVersion);
131+
pcre2_version(sPcre2Version, 256);
132+
call_eSoftVersion_setfields(sZlibVersion, sPcre2Version);
117133
}
118134

119135
int call_base_umask(int mode) {

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