##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.38.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gdsfmt.buildbin-libdir gdsfmt_1.38.0.tar.gz'
>>>>>>>
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gdsfmt.cpp -o gdsfmt.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c digest.cpp -o digest.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o
ZLIB/adler32.c:63:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32_z(adler, buf, len)
^
ZLIB/adler32.c:134:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32(adler, buf, len)
^
ZLIB/adler32.c:143:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local uLong adler32_combine_(adler1, adler2, len2)
^
ZLIB/adler32.c:172:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32_combine(adler1, adler2, len2)
^
ZLIB/adler32.c:180:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT adler32_combine64(adler1, adler2, len2)
^
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/compress.c -o ZLIB/compress.o
ZLIB/compress.c:22:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT compress2(dest, destLen, source, sourceLen, level)
^
ZLIB/compress.c:68:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT compress(dest, destLen, source, sourceLen)
^
ZLIB/compress.c:81:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT compressBound(sourceLen)
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o
ZLIB/crc32.c:551:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local z_crc_t multmodp(a, b)
^
ZLIB/crc32.c:575:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local z_crc_t x2nmodp(n, k)
^
ZLIB/crc32.c:622:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
unsigned long ZEXPORT crc32_z(crc, buf, len)
^
ZLIB/crc32.c:1072:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
unsigned long ZEXPORT crc32(crc, buf, len)
^
ZLIB/crc32.c:1081:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine64(crc1, crc2, len2)
^
ZLIB/crc32.c:1093:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine(crc1, crc2, len2)
^
ZLIB/crc32.c:1102:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine_gen64(len2)
^
ZLIB/crc32.c:1112:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine_gen(len2)
^
ZLIB/crc32.c:1119:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT crc32_combine_op(crc1, crc2, op)
^
9 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o
ZLIB/deflate.c:198:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void slide_hash(s)
^
ZLIB/deflate.c:225:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateInit_(strm, level, version, stream_size)
^
ZLIB/deflate.c:237:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
^
ZLIB/deflate.c:389:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int deflateStateCheck(strm)
^
ZLIB/deflate.c:412:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateSetDictionary(strm, dictionary, dictLength)
^
ZLIB/deflate.c:481:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateGetDictionary(strm, dictionary, dictLength)
^
ZLIB/deflate.c:503:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateResetKeep(strm)
^
ZLIB/deflate.c:541:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateReset(strm)
^
ZLIB/deflate.c:553:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateSetHeader(strm, head)
^
ZLIB/deflate.c:564:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflatePending(strm, pending, bits)
^
ZLIB/deflate.c:578:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflatePrime(strm, bits, value)
^
ZLIB/deflate.c:605:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateParams(strm, level, strategy)
^
ZLIB/deflate.c:654:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
^
ZLIB/deflate.c:696:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
uLong ZEXPORT deflateBound(strm, sourceLen)
^
ZLIB/deflate.c:768:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void putShortMSB(s, b)
^
ZLIB/deflate.c:782:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void flush_pending(strm)
^
ZLIB/deflate.c:815:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflate(strm, flush)
^
ZLIB/deflate.c:1130:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateEnd(strm)
^
ZLIB/deflate.c:1156:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT deflateCopy(dest, source)
^
ZLIB/deflate.c:1215:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned read_buf(strm, buf, size)
^
ZLIB/deflate.c:1245:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void lm_init(s)
^
ZLIB/deflate.c:1278:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local uInt longest_match(s, cur_match)
^
ZLIB/deflate.c:1527:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fill_window(s)
^
ZLIB/deflate.c:1690:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_stored(s, flush)
^
ZLIB/deflate.c:1877:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_fast(s, flush)
^
ZLIB/deflate.c:1979:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_slow(s, flush)
^
ZLIB/deflate.c:2110:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_rle(s, flush)
^
ZLIB/deflate.c:2184:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local block_state deflate_huff(s, flush)
^
28 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/infback.c -o ZLIB/infback.o
ZLIB/infback.c:28:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
^
ZLIB/infback.c:83:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fixedtables(state)
^
ZLIB/infback.c:251:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
^
ZLIB/infback.c:635:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateBackEnd(strm)
^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o
ZLIB/inffast.c:50:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL inflate_fast(strm, start)
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o
ZLIB/inflate.c:105:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int inflateStateCheck(strm)
^
ZLIB/inflate.c:119:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateResetKeep(strm)
^
ZLIB/inflate.c:145:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateReset(strm)
^
ZLIB/inflate.c:158:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateReset2(strm, windowBits)
^
ZLIB/inflate.c:198:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
^
ZLIB/inflate.c:242:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateInit_(strm, version, stream_size)
^
ZLIB/inflate.c:250:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflatePrime(strm, bits, value)
^
ZLIB/inflate.c:281:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void fixedtables(state)
^
ZLIB/inflate.c:399:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int updatewindow(strm, end, copy)
^
ZLIB/inflate.c:625:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflate(strm, flush)
^
ZLIB/inflate.c:1304:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateEnd(strm)
^
ZLIB/inflate.c:1318:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateGetDictionary(strm, dictionary, dictLength)
^
ZLIB/inflate.c:1341:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
^
ZLIB/inflate.c:1376:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateGetHeader(strm, head)
^
ZLIB/inflate.c:1404:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned syncsearch(have, buf, len)
^
ZLIB/inflate.c:1427:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSync(strm)
^
ZLIB/inflate.c:1485:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateSyncPoint(strm)
^
ZLIB/inflate.c:1495:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateCopy(dest, source)
^
ZLIB/inflate.c:1542:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateUndermine(strm, subvert)
^
ZLIB/inflate.c:1560:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT inflateValidate(strm, check)
^
ZLIB/inflate.c:1575:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
long ZEXPORT inflateMark(strm)
^
ZLIB/inflate.c:1588:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
unsigned long ZEXPORT inflateCodesUsed(strm)
^
22 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o
ZLIB/inftrees.c:32:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work)
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/trees.c -o ZLIB/trees.o
ZLIB/trees.c:379:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL _tr_init(s)
^
ZLIB/trees.c:407:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void init_block(s)
^
ZLIB/trees.c:451:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void pqdownheap(s, tree, k)
^
ZLIB/trees.c:486:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void gen_bitlen(s, desc)
^
ZLIB/trees.c:572:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void gen_codes(tree, max_code, bl_count)
^
ZLIB/trees.c:615:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void build_tree(s, desc)
^
ZLIB/trees.c:703:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void scan_tree(s, tree, max_code)
^
ZLIB/trees.c:748:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void send_tree(s, tree, max_code)
^
ZLIB/trees.c:799:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int build_bl_tree(s)
^
ZLIB/trees.c:834:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void send_all_trees(s, lcodes, dcodes, blcodes)
^
ZLIB/trees.c:863:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL _tr_stored_block(s, buf, stored_len, last)
^
ZLIB/trees.c:887:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL _tr_flush_bits(s)
^
ZLIB/trees.c:897:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL _tr_align(s)
^
ZLIB/trees.c:912:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL _tr_flush_block(s, buf, stored_len, last)
^
ZLIB/trees.c:1014:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZLIB_INTERNAL _tr_tally(s, dist, lc)
^
ZLIB/trees.c:1042:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void compress_block(s, ltree, dtree)
^
ZLIB/trees.c:1102:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local int detect_data_type(s)
^
ZLIB/trees.c:1136:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local unsigned bi_reverse(code, len)
^
ZLIB/trees.c:1151:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void bi_flush(s)
^
ZLIB/trees.c:1168:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
local void bi_windup(s)
^
20 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o
ZLIB/uncompr.c:27:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT uncompress2(dest, destLen, source, sourceLen)
^
ZLIB/uncompr.c:86:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int ZEXPORT uncompress(dest, destLen, source, sourceLen)
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o
ZLIB/zutil.c:136:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
const char * ZEXPORT zError(err)
^
ZLIB/zutil.c:308:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
voidpf ZLIB_INTERNAL zcalloc(opaque, items, size)
^
ZLIB/zutil.c:318:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void ZLIB_INTERNAL zcfree(opaque, ptr)
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4.c -o LZ4/lz4.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4hc.c -o LZ4/lz4hc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4frame.c -o LZ4/lz4frame.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.9.tar.gz
cd XZ/xz-5.2.9 && \
./configure CC="clang -arch arm64" CPP="clang -arch arm64 -E" CXX="clang++ -arch arm64 -std=gnu++17" CXXCPP="" --build="" \
--with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null
cd XZ/xz-5.2.9/src/liblzma && make
Making all in api
make[2]: Nothing to be done for `all'.
CC liblzma_la-tuklib_physmem.lo
CC liblzma_la-tuklib_cpucores.lo
CC liblzma_la-common.lo
CC liblzma_la-block_util.lo
CC liblzma_la-easy_preset.lo
CC liblzma_la-filter_common.lo
CC liblzma_la-hardware_physmem.lo
CC liblzma_la-index.lo
CC liblzma_la-stream_flags_common.lo
CC liblzma_la-vli_size.lo
CC liblzma_la-hardware_cputhreads.lo
CC liblzma_la-alone_encoder.lo
CC liblzma_la-block_buffer_encoder.lo
CC liblzma_la-block_encoder.lo
CC liblzma_la-block_header_encoder.lo
CC liblzma_la-easy_buffer_encoder.lo
CC liblzma_la-easy_encoder.lo
CC liblzma_la-easy_encoder_memusage.lo
CC liblzma_la-filter_buffer_encoder.lo
CC liblzma_la-filter_encoder.lo
CC liblzma_la-filter_flags_encoder.lo
CC liblzma_la-index_encoder.lo
CC liblzma_la-stream_buffer_encoder.lo
CC liblzma_la-stream_encoder.lo
CC liblzma_la-stream_flags_encoder.lo
CC liblzma_la-vli_encoder.lo
CC liblzma_la-outqueue.lo
CC liblzma_la-stream_encoder_mt.lo
CC liblzma_la-alone_decoder.lo
CC liblzma_la-auto_decoder.lo
CC liblzma_la-block_buffer_decoder.lo
CC liblzma_la-block_decoder.lo
CC liblzma_la-block_header_decoder.lo
CC liblzma_la-easy_decoder_memusage.lo
CC liblzma_la-filter_buffer_decoder.lo
CC liblzma_la-filter_decoder.lo
CC liblzma_la-filter_flags_decoder.lo
CC liblzma_la-index_decoder.lo
CC liblzma_la-index_hash.lo
CC liblzma_la-stream_buffer_decoder.lo
CC liblzma_la-stream_decoder.lo
CC liblzma_la-stream_flags_decoder.lo
CC liblzma_la-vli_decoder.lo
CC liblzma_la-check.lo
CC liblzma_la-crc32_table.lo
CC liblzma_la-crc32_fast.lo
CC liblzma_la-crc64_table.lo
CC liblzma_la-crc64_fast.lo
CC liblzma_la-sha256.lo
CC liblzma_la-lz_encoder.lo
CC liblzma_la-lz_encoder_mf.lo
CC liblzma_la-lz_decoder.lo
CC liblzma_la-lzma_encoder_presets.lo
CC liblzma_la-lzma_encoder.lo
CC liblzma_la-lzma_encoder_optimum_fast.lo
CC liblzma_la-lzma_encoder_optimum_normal.lo
CC liblzma_la-fastpos_table.lo
CC liblzma_la-lzma_decoder.lo
CC liblzma_la-lzma2_encoder.lo
CC liblzma_la-lzma2_decoder.lo
CC liblzma_la-price_table.lo
CC liblzma_la-delta_common.lo
CC liblzma_la-delta_encoder.lo
CC liblzma_la-delta_decoder.lo
CC liblzma_la-simple_coder.lo
CC liblzma_la-simple_encoder.lo
CC liblzma_la-simple_decoder.lo
CC liblzma_la-x86.lo
CC liblzma_la-powerpc.lo
CC liblzma_la-ia64.lo
CC liblzma_la-arm.lo
CC liblzma_la-armthumb.lo
CC liblzma_la-sparc.lo
CCLD liblzma.la
PC liblzma.pc
cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a .
rm -rf XZ/xz-5.2.9/dos
rm -rf XZ/xz-5.2.9/po
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gdsfmt.buildbin-libdir/00LOCK-gdsfmt/00new/gdsfmt/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gdsfmt)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so
>>>>>>>
>>>>>>> Paths before fix:
gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so:
gdsfmt.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so"
>>>>>>> Paths after fix:
gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so:
gdsfmt.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
