############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf chopsticks.buildbin-libdir && mkdir chopsticks.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chopsticks_1.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R chopsticks.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chopsticks.buildbin-libdir chopsticks_1.70.0.tar.gz' >>>>>>> * installing *source* package ‘chopsticks’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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] (iter && (abs(wss-wss_last)/wss_last < conv)); ^ glm_test.c:155:14: note: use function 'fabs' instead (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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 inputNew.c:612:17: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] Rprintf("%d polymorphisms were not SNPs and have been set to NA "); ~^ 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_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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 C2x [-Wdeprecated-non-prototype] 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 -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/chopsticks.buildbin-libdir/00LOCK-chopsticks/00new/chopsticks/libs ** R ** data ** 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 (chopsticks) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so >>>>>>> >>>>>>> Paths before fix: chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so: chopsticks.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so" >>>>>>> Paths after fix: chopsticks.buildbin-libdir/chopsticks/libs/chopsticks.so: chopsticks.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)