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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chopsticks
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘chopsticks’ ...
** this is package ‘chopsticks’ version ‘1.77.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c adler32.c -o adler32.o
adler32.c:57:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
57 | uLong ZEXPORT adler32(adler, buf, len)
| ^
adler32.c:128:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
128 | uLong ZEXPORT adler32_combine(adler1, adler2, len2)
| ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bind.c -o bind.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compress.c -o compress.o
compress.c:22:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
22 | int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
| ^
compress.c:62:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
62 | int ZEXPORT compress (dest, destLen, source, sourceLen)
| ^
compress.c:75:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
75 | uLong ZEXPORT compressBound (sourceLen)
| ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crc32.c -o crc32.o
crc32.c:219:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
219 | unsigned long ZEXPORT crc32(crc, buf, len)
| ^
crc32.c:262:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
262 | local unsigned long crc32_little(crc, buf, len)
| ^
crc32.c:302:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
302 | local unsigned long crc32_big(crc, buf, len)
| ^
crc32.c:342:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
342 | local unsigned long gf2_matrix_times(mat, vec)
| ^
crc32.c:359:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
359 | local void gf2_matrix_square(square, mat)
| ^
crc32.c:370:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
370 | uLong ZEXPORT crc32_combine(crc1, crc2, len2)
| ^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c deflate.c -o deflate.o
deflate.c:204:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
204 | int ZEXPORT deflateInit_(strm, level, version, stream_size)
| ^
deflate.c:216:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
216 | int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
| ^
deflate.c:315:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
315 | int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
| ^
deflate.c:357:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
357 | int ZEXPORT deflateReset (strm)
| ^
deflate.c:393:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
393 | int ZEXPORT deflateSetHeader (strm, head)
| ^
deflate.c:404:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
404 | int ZEXPORT deflatePrime (strm, bits, value)
| ^
deflate.c:416:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
416 | int ZEXPORT deflateParams(strm, level, strategy)
| ^
deflate.c:454:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
454 | int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
| ^
deflate.c:489:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
489 | uLong ZEXPORT deflateBound(strm, sourceLen)
| ^
deflate.c:518:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
518 | local void putShortMSB (s, b)
| ^
deflate.c:532:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
532 | local void flush_pending(strm)
| ^
deflate.c:552:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
552 | int ZEXPORT deflate (strm, flush)
| ^
deflate.c:859:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
859 | int ZEXPORT deflateEnd (strm)
| ^
deflate.c:894:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
894 | int ZEXPORT deflateCopy (dest, source)
| ^
deflate.c:956:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
956 | local int read_buf(strm, buf, size)
| ^
deflate.c:986:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
986 | local void lm_init (s)
| ^
deflate.c:1027:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1027 | local uInt longest_match(s, cur_match)
| ^
deflate.c:1175:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1175 | local uInt longest_match_fast(s, cur_match)
| ^
deflate.c:1266:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1266 | local void fill_window(s)
| ^
deflate.c:1390:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1390 | local block_state deflate_stored(s, flush)
| ^
deflate.c:1448:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1448 | local block_state deflate_fast(s, flush)
| ^
deflate.c:1554:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1554 | local block_state deflate_slow(s, flush)
| ^
22 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c force_hom.c -o force_hom.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_test.c -o glm_test.o
glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
155 | (iter && (abs(wss-wss_last)/wss_last < conv));
| ^
glm_test.c:155:14: note: use function 'fabs' instead
155 | (iter && (abs(wss-wss_last)/wss_last < conv));
| ^~~
| fabs
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_test_R.c -o glm_test_R.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gzio.c -o gzio.o
gzio.c:93:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
93 | local gzFile gz_open (path, mode, fd)
| ^
gzio.c:208:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
208 | gzFile ZEXPORT gzopen (path, mode)
| ^
gzio.c:219:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
219 | gzFile ZEXPORT gzdopen (fd, mode)
| ^
gzio.c:234:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
234 | int ZEXPORT gzsetparams (file, level, strategy)
| ^
gzio.c:261:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
261 | local int get_byte(s)
| ^
gzio.c:288:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
288 | local void check_header(s)
| ^
gzio.c:355:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
355 | local int destroy (s)
| ^
gzio.c:394:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
394 | int ZEXPORT gzread (file, buf, len)
| ^
gzio.c:503:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
503 | int ZEXPORT gzgetc(file)
| ^
gzio.c:515:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
515 | int ZEXPORT gzungetc(c, file)
| ^
gzio.c:540:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
540 | char * ZEXPORT gzgets(file, buf, len)
| ^
gzio.c:559:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
559 | int ZEXPORT gzwrite (file, buf, len)
| ^
gzio.c:678:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
678 | int ZEXPORT gzputc(file, c)
| ^
gzio.c:693:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
693 | int ZEXPORT gzputs(file, s)
| ^
gzio.c:705:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
705 | local int do_flush (file, flush)
| ^
gzio.c:746:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
746 | int ZEXPORT gzflush (file, flush)
| ^
gzio.c:767:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
767 | z_off_t ZEXPORT gzseek (file, offset, whence)
| ^
gzio.c:857:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
857 | int ZEXPORT gzrewind (file)
| ^
gzio.c:881:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
881 | z_off_t ZEXPORT gztell (file)
| ^
gzio.c:891:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
891 | int ZEXPORT gzeof (file)
| ^
gzio.c:908:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
908 | int ZEXPORT gzdirect (file)
| ^
gzio.c:920:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
920 | local void putLong (file, x)
| ^
gzio.c:935:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
935 | local uLong getLong (s)
| ^
gzio.c:953:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
953 | int ZEXPORT gzclose (file)
| ^
gzio.c:987:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
987 | const char * ZEXPORT gzerror (file, errnum)
| ^
gzio.c:1017:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1017 | void ZEXPORT gzclearerr (file)
| ^
26 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hash_index.c -o hash_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ibs.c -o ibs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c in.c -o in.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c infback.c -o infback.o
infback.c:28:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
28 | int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
| ^
infback.c:73:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
73 | local void fixedtables(state)
| ^
infback.c:241:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
241 | int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
| ^
infback.c:614:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
614 | int ZEXPORT inflateBackEnd(strm)
| ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inffast.c -o inffast.o
inffast.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
67 | void inflate_fast(strm, start)
| ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inflate.c -o inflate.o
inflate.c:103:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
103 | int ZEXPORT inflateReset(strm)
| ^
inflate.c:128:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
128 | int ZEXPORT inflatePrime(strm, bits, value)
| ^
inflate.c:144:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
144 | int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
| ^
inflate.c:187:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
187 | int ZEXPORT inflateInit_(strm, version, stream_size)
| ^
inflate.c:205:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
205 | local void fixedtables(state)
| ^
inflate.c:323:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
323 | local int updatewindow(strm, out)
| ^
inflate.c:554:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
554 | int ZEXPORT inflate(strm, flush)
| ^
inflate.c:1155:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1155 | int ZEXPORT inflateEnd(strm)
| ^
inflate.c:1169:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1169 | int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
| ^
inflate.c:1211:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1211 | int ZEXPORT inflateGetHeader(strm, head)
| ^
inflate.c:1239:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1239 | local unsigned syncsearch(have, buf, len)
| ^
inflate.c:1262:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1262 | int ZEXPORT inflateSync(strm)
| ^
inflate.c:1313:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1313 | int ZEXPORT inflateSyncPoint(strm)
| ^
inflate.c:1323:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1323 | int ZEXPORT inflateCopy(dest, source)
| ^
14 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inftrees.c -o inftrees.o
inftrees.c:32:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
32 | int inflate_table(type, lens, codes, table, bits, work)
| ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c input.c -o input.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inputNew.c -o inputNew.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c input_unsorted.c -o input_unsorted.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ld_graphic_eps.c -o ld_graphic_eps.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ld_with.c -o ld_with.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mla.c -o mla.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c outdata.c -o outdata.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise_linkage.c -o pairwise_linkage.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_chiamo.c -o read_chiamo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_hapmap.c -o read_hapmap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_pedfile.c -o read_pedfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_signals.c -o read_signals.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readped.c -o readped.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sdfpw.c -o sdfpw.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c single_snp_tests.c -o single_snp_tests.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c snp_summary.c -o snp_summary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c snpmpy.c -o snpmpy.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c solve_cubic.c -o solve_cubic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c solve_quadratic.c -o solve_quadratic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c structure.c -o structure.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trees.c -o trees.o
trees.c:382:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
382 | void _tr_init(s)
| ^
trees.c:411:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
411 | local void init_block(s)
| ^
trees.c:455:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
455 | local void pqdownheap(s, tree, k)
| ^
trees.c:490:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
490 | local void gen_bitlen(s, desc)
| ^
trees.c:577:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
577 | local void gen_codes (tree, max_code, bl_count)
| ^
trees.c:619:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
619 | local void build_tree(s, desc)
| ^
trees.c:707:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
707 | local void scan_tree (s, tree, max_code)
| ^
trees.c:752:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
752 | local void send_tree (s, tree, max_code)
| ^
trees.c:803:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
803 | local int build_bl_tree(s)
| ^
trees.c:838:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
838 | local void send_all_trees(s, lcodes, dcodes, blcodes)
| ^
trees.c:867:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
867 | void _tr_stored_block(s, buf, stored_len, eof)
| ^
trees.c:892:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
892 | void _tr_align(s)
| ^
trees.c:921:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
921 | void _tr_flush_block(s, buf, stored_len, eof)
| ^
trees.c:1022:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1022 | int _tr_tally (s, dist, lc)
| ^
trees.c:1072:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1072 | local void compress_block(s, ltree, dtree)
| ^
trees.c:1126:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1126 | local void set_data_type(s)
| ^
trees.c:1146:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1146 | local unsigned bi_reverse(code, len)
| ^
trees.c:1161:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1161 | local void bi_flush(s)
| ^
trees.c:1178:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1178 | local void bi_windup(s)
| ^
trees.c:1197:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1197 | local void copy_block(s, buf, len, header)
| ^
20 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uncompr.c -o uncompr.o
uncompr.c:26:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
26 | int ZEXPORT uncompress (dest, destLen, source, sourceLen)
| ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c zutil.c -o zutil.o
zutil.c:133:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
133 | const char * ZEXPORT zError(err)
| ^
zutil.c:300:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
300 | voidpf zcalloc (opaque, items, size)
| ^
zutil.c:310:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
310 | void zcfree (opaque, ptr)
| ^
3 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chopsticks.so adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-chopsticks/00new/chopsticks/libs
** R
** data
** 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 (chopsticks)
