############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf chopsticks.buildbin-libdir && mkdir chopsticks.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=chopsticks.buildbin-libdir chopsticks_1.73.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'chopsticks' ... ** this is package 'chopsticks' version '1.73.0' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c adler32.c -o adler32.o adler32.c: In function 'adler32': adler32.c:57:15: warning: old-style function definition [-Wold-style-definition] 57 | uLong ZEXPORT adler32(adler, buf, len) | ^~~~~~~ adler32.c: In function 'adler32_combine': adler32.c:128:15: warning: old-style function definition [-Wold-style-definition] 128 | uLong ZEXPORT adler32_combine(adler1, adler2, len2) | ^~~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c bind.c -o bind.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c compress.c -o compress.o compress.c: In function 'compress2': compress.c:22:13: warning: old-style function definition [-Wold-style-definition] 22 | int ZEXPORT compress2 (dest, destLen, source, sourceLen, level) | ^~~~~~~~~ compress.c: In function 'compress': compress.c:62:13: warning: old-style function definition [-Wold-style-definition] 62 | int ZEXPORT compress (dest, destLen, source, sourceLen) | ^~~~~~~~ compress.c: In function 'compressBound': compress.c:75:15: warning: old-style function definition [-Wold-style-definition] 75 | uLong ZEXPORT compressBound (sourceLen) | ^~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c crc32.c -o crc32.o crc32.c: In function 'crc32': crc32.c:219:23: warning: old-style function definition [-Wold-style-definition] 219 | unsigned long ZEXPORT crc32(crc, buf, len) | ^~~~~ crc32.c: In function 'crc32_little': crc32.c:262:21: warning: old-style function definition [-Wold-style-definition] 262 | local unsigned long crc32_little(crc, buf, len) | ^~~~~~~~~~~~ crc32.c: In function 'crc32_big': crc32.c:302:21: warning: old-style function definition [-Wold-style-definition] 302 | local unsigned long crc32_big(crc, buf, len) | ^~~~~~~~~ crc32.c: In function 'gf2_matrix_times': crc32.c:342:21: warning: old-style function definition [-Wold-style-definition] 342 | local unsigned long gf2_matrix_times(mat, vec) | ^~~~~~~~~~~~~~~~ crc32.c: In function 'gf2_matrix_square': crc32.c:359:12: warning: old-style function definition [-Wold-style-definition] 359 | local void gf2_matrix_square(square, mat) | ^~~~~~~~~~~~~~~~~ crc32.c: In function 'crc32_combine': crc32.c:370:15: warning: old-style function definition [-Wold-style-definition] 370 | uLong ZEXPORT crc32_combine(crc1, crc2, len2) | ^~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c deflate.c -o deflate.o deflate.c: In function 'deflateInit_': deflate.c:204:13: warning: old-style function definition [-Wold-style-definition] 204 | int ZEXPORT deflateInit_(strm, level, version, stream_size) | ^~~~~~~~~~~~ deflate.c: In function 'deflateInit2_': deflate.c:216:13: warning: old-style function definition [-Wold-style-definition] 216 | int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy, | ^~~~~~~~~~~~~ deflate.c: In function 'deflateSetDictionary': deflate.c:315:13: warning: old-style function definition [-Wold-style-definition] 315 | int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength) | ^~~~~~~~~~~~~~~~~~~~ deflate.c: In function 'deflateReset': deflate.c:357:13: warning: old-style function definition [-Wold-style-definition] 357 | int ZEXPORT deflateReset (strm) | ^~~~~~~~~~~~ deflate.c: In function 'deflateSetHeader': deflate.c:393:13: warning: old-style function definition [-Wold-style-definition] 393 | int ZEXPORT deflateSetHeader (strm, head) | ^~~~~~~~~~~~~~~~ deflate.c: In function 'deflatePrime': deflate.c:404:13: warning: old-style function definition [-Wold-style-definition] 404 | int ZEXPORT deflatePrime (strm, bits, value) | ^~~~~~~~~~~~ deflate.c: In function 'deflateParams': deflate.c:416:13: warning: old-style function definition [-Wold-style-definition] 416 | int ZEXPORT deflateParams(strm, level, strategy) | ^~~~~~~~~~~~~ deflate.c: In function 'deflateTune': deflate.c:454:13: warning: old-style function definition [-Wold-style-definition] 454 | int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain) | ^~~~~~~~~~~ deflate.c: In function 'deflateBound': deflate.c:489:15: warning: old-style function definition [-Wold-style-definition] 489 | uLong ZEXPORT deflateBound(strm, sourceLen) | ^~~~~~~~~~~~ deflate.c: In function 'putShortMSB': deflate.c:518:12: warning: old-style function definition [-Wold-style-definition] 518 | local void putShortMSB (s, b) | ^~~~~~~~~~~ deflate.c: In function 'flush_pending': deflate.c:532:12: warning: old-style function definition [-Wold-style-definition] 532 | local void flush_pending(strm) | ^~~~~~~~~~~~~ deflate.c: In function 'deflate': deflate.c:552:13: warning: old-style function definition [-Wold-style-definition] 552 | int ZEXPORT deflate (strm, flush) | ^~~~~~~ deflate.c: In function 'deflateEnd': deflate.c:859:13: warning: old-style function definition [-Wold-style-definition] 859 | int ZEXPORT deflateEnd (strm) | ^~~~~~~~~~ deflate.c: In function 'deflateCopy': deflate.c:894:13: warning: old-style function definition [-Wold-style-definition] 894 | int ZEXPORT deflateCopy (dest, source) | ^~~~~~~~~~~ deflate.c: In function 'read_buf': deflate.c:956:11: warning: old-style function definition [-Wold-style-definition] 956 | local int read_buf(strm, buf, size) | ^~~~~~~~ deflate.c: In function 'lm_init': deflate.c:986:12: warning: old-style function definition [-Wold-style-definition] 986 | local void lm_init (s) | ^~~~~~~ deflate.c: In function 'longest_match': deflate.c:1027:12: warning: old-style function definition [-Wold-style-definition] 1027 | local uInt longest_match(s, cur_match) | ^~~~~~~~~~~~~ deflate.c: In function 'longest_match_fast': deflate.c:1175:12: warning: old-style function definition [-Wold-style-definition] 1175 | local uInt longest_match_fast(s, cur_match) | ^~~~~~~~~~~~~~~~~~ deflate.c: In function 'fill_window': deflate.c:1266:12: warning: old-style function definition [-Wold-style-definition] 1266 | local void fill_window(s) | ^~~~~~~~~~~ deflate.c: In function 'deflate_stored': deflate.c:1390:19: warning: old-style function definition [-Wold-style-definition] 1390 | local block_state deflate_stored(s, flush) | ^~~~~~~~~~~~~~ deflate.c: In function 'deflate_fast': deflate.c:1448:19: warning: old-style function definition [-Wold-style-definition] 1448 | local block_state deflate_fast(s, flush) | ^~~~~~~~~~~~ deflate.c: In function 'deflate_slow': deflate.c:1554:19: warning: old-style function definition [-Wold-style-definition] 1554 | local block_state deflate_slow(s, flush) | ^~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c force_hom.c -o force_hom.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c glm_test.c -o glm_test.o glm_test.c: In function 'glm_fit': glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | double *yw = (double *) calloc(N, sizeof(double)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from glm_test.c:1: C:/rtools45/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here 536 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | double *yw = (double *) calloc(N, sizeof(double)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools45/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here 536 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c glm_test_R.c -o glm_test_R.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c gzio.c -o gzio.o gzio.c: In function 'gz_open': gzio.c:93:14: warning: old-style function definition [-Wold-style-definition] 93 | local gzFile gz_open (path, mode, fd) | ^~~~~~~ gzio.c: In function 'gzopen': gzio.c:208:16: warning: old-style function definition [-Wold-style-definition] 208 | gzFile ZEXPORT gzopen (path, mode) | ^~~~~~ gzio.c: In function 'gzdopen': gzio.c:219:16: warning: old-style function definition [-Wold-style-definition] 219 | gzFile ZEXPORT gzdopen (fd, mode) | ^~~~~~~ gzio.c: In function 'gzsetparams': gzio.c:234:13: warning: old-style function definition [-Wold-style-definition] 234 | int ZEXPORT gzsetparams (file, level, strategy) | ^~~~~~~~~~~ gzio.c: In function 'get_byte': gzio.c:261:11: warning: old-style function definition [-Wold-style-definition] 261 | local int get_byte(s) | ^~~~~~~~ gzio.c: In function 'check_header': gzio.c:288:12: warning: old-style function definition [-Wold-style-definition] 288 | local void check_header(s) | ^~~~~~~~~~~~ gzio.c: In function 'destroy': gzio.c:355:11: warning: old-style function definition [-Wold-style-definition] 355 | local int destroy (s) | ^~~~~~~ gzio.c: In function 'gzread': gzio.c:394:13: warning: old-style function definition [-Wold-style-definition] 394 | int ZEXPORT gzread (file, buf, len) | ^~~~~~ gzio.c: In function 'gzgetc': gzio.c:503:13: warning: old-style function definition [-Wold-style-definition] 503 | int ZEXPORT gzgetc(file) | ^~~~~~ gzio.c: In function 'gzungetc': gzio.c:515:13: warning: old-style function definition [-Wold-style-definition] 515 | int ZEXPORT gzungetc(c, file) | ^~~~~~~~ gzio.c: In function 'gzgets': gzio.c:540:16: warning: old-style function definition [-Wold-style-definition] 540 | char * ZEXPORT gzgets(file, buf, len) | ^~~~~~ gzio.c: In function 'gzwrite': gzio.c:559:13: warning: old-style function definition [-Wold-style-definition] 559 | int ZEXPORT gzwrite (file, buf, len) | ^~~~~~~ gzio.c: In function 'gzputc': gzio.c:678:13: warning: old-style function definition [-Wold-style-definition] 678 | int ZEXPORT gzputc(file, c) | ^~~~~~ gzio.c: In function 'gzputs': gzio.c:693:13: warning: old-style function definition [-Wold-style-definition] 693 | int ZEXPORT gzputs(file, s) | ^~~~~~ gzio.c: In function 'do_flush': gzio.c:705:11: warning: old-style function definition [-Wold-style-definition] 705 | local int do_flush (file, flush) | ^~~~~~~~ gzio.c: In function 'gzflush': gzio.c:746:13: warning: old-style function definition [-Wold-style-definition] 746 | int ZEXPORT gzflush (file, flush) | ^~~~~~~ gzio.c: In function 'gzseek': gzio.c:767:17: warning: old-style function definition [-Wold-style-definition] 767 | z_off_t ZEXPORT gzseek (file, offset, whence) | ^~~~~~ gzio.c: In function 'gzrewind': gzio.c:857:13: warning: old-style function definition [-Wold-style-definition] 857 | int ZEXPORT gzrewind (file) | ^~~~~~~~ gzio.c: In function 'gztell': gzio.c:881:17: warning: old-style function definition [-Wold-style-definition] 881 | z_off_t ZEXPORT gztell (file) | ^~~~~~ gzio.c: In function 'gzeof': gzio.c:891:13: warning: old-style function definition [-Wold-style-definition] 891 | int ZEXPORT gzeof (file) | ^~~~~ gzio.c: In function 'gzdirect': gzio.c:908:13: warning: old-style function definition [-Wold-style-definition] 908 | int ZEXPORT gzdirect (file) | ^~~~~~~~ gzio.c: In function 'putLong': gzio.c:920:12: warning: old-style function definition [-Wold-style-definition] 920 | local void putLong (file, x) | ^~~~~~~ gzio.c: In function 'getLong': gzio.c:935:13: warning: old-style function definition [-Wold-style-definition] 935 | local uLong getLong (s) | ^~~~~~~ gzio.c: In function 'gzclose': gzio.c:953:13: warning: old-style function definition [-Wold-style-definition] 953 | int ZEXPORT gzclose (file) | ^~~~~~~ gzio.c: In function 'gzerror': gzio.c:987:22: warning: old-style function definition [-Wold-style-definition] 987 | const char * ZEXPORT gzerror (file, errnum) | ^~~~~~~ gzio.c: In function 'gzclearerr': gzio.c:1017:14: warning: old-style function definition [-Wold-style-definition] 1017 | void ZEXPORT gzclearerr (file) | ^~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c hash_index.c -o hash_index.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ibs.c -o ibs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c in.c -o in.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c infback.c -o infback.o infback.c: In function 'inflateBackInit_': infback.c:28:13: warning: old-style function definition [-Wold-style-definition] 28 | int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size) | ^~~~~~~~~~~~~~~~ infback.c: In function 'fixedtables': infback.c:73:12: warning: old-style function definition [-Wold-style-definition] 73 | local void fixedtables(state) | ^~~~~~~~~~~ infback.c: In function 'inflateBack': infback.c:241:13: warning: old-style function definition [-Wold-style-definition] 241 | int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc) | ^~~~~~~~~~~ infback.c: In function 'inflateBackEnd': infback.c:614:13: warning: old-style function definition [-Wold-style-definition] 614 | int ZEXPORT inflateBackEnd(strm) | ^~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c inffast.c -o inffast.o inffast.c: In function 'inflate_fast': inffast.c:67:6: warning: old-style function definition [-Wold-style-definition] 67 | void inflate_fast(strm, start) | ^~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c inflate.c -o inflate.o inflate.c: In function 'inflateReset': inflate.c:103:13: warning: old-style function definition [-Wold-style-definition] 103 | int ZEXPORT inflateReset(strm) | ^~~~~~~~~~~~ inflate.c: In function 'inflatePrime': inflate.c:128:13: warning: old-style function definition [-Wold-style-definition] 128 | int ZEXPORT inflatePrime(strm, bits, value) | ^~~~~~~~~~~~ inflate.c: In function 'inflateInit2_': inflate.c:144:13: warning: old-style function definition [-Wold-style-definition] 144 | int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size) | ^~~~~~~~~~~~~ inflate.c: In function 'inflateInit_': inflate.c:187:13: warning: old-style function definition [-Wold-style-definition] 187 | int ZEXPORT inflateInit_(strm, version, stream_size) | ^~~~~~~~~~~~ inflate.c: In function 'fixedtables': inflate.c:205:12: warning: old-style function definition [-Wold-style-definition] 205 | local void fixedtables(state) | ^~~~~~~~~~~ inflate.c: In function 'updatewindow': inflate.c:323:11: warning: old-style function definition [-Wold-style-definition] 323 | local int updatewindow(strm, out) | ^~~~~~~~~~~~ inflate.c: In function 'inflate': inflate.c:554:13: warning: old-style function definition [-Wold-style-definition] 554 | int ZEXPORT inflate(strm, flush) | ^~~~~~~ inflate.c: In function 'inflateEnd': inflate.c:1155:13: warning: old-style function definition [-Wold-style-definition] 1155 | int ZEXPORT inflateEnd(strm) | ^~~~~~~~~~ inflate.c: In function 'inflateSetDictionary': inflate.c:1169:13: warning: old-style function definition [-Wold-style-definition] 1169 | int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength) | ^~~~~~~~~~~~~~~~~~~~ inflate.c: In function 'inflateGetHeader': inflate.c:1211:13: warning: old-style function definition [-Wold-style-definition] 1211 | int ZEXPORT inflateGetHeader(strm, head) | ^~~~~~~~~~~~~~~~ inflate.c: In function 'syncsearch': inflate.c:1239:16: warning: old-style function definition [-Wold-style-definition] 1239 | local unsigned syncsearch(have, buf, len) | ^~~~~~~~~~ inflate.c: In function 'inflateSync': inflate.c:1262:13: warning: old-style function definition [-Wold-style-definition] 1262 | int ZEXPORT inflateSync(strm) | ^~~~~~~~~~~ inflate.c: In function 'inflateSyncPoint': inflate.c:1313:13: warning: old-style function definition [-Wold-style-definition] 1313 | int ZEXPORT inflateSyncPoint(strm) | ^~~~~~~~~~~~~~~~ inflate.c: In function 'inflateCopy': inflate.c:1323:13: warning: old-style function definition [-Wold-style-definition] 1323 | int ZEXPORT inflateCopy(dest, source) | ^~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c inftrees.c -o inftrees.o inftrees.c: In function 'inflate_table': inftrees.c:32:5: warning: old-style function definition [-Wold-style-definition] 32 | int inflate_table(type, lens, codes, table, bits, work) | ^~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c input.c -o input.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c inputNew.c -o inputNew.o inputNew.c: In function 'simplify_names': inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 687 | strncpy(back, front, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c: In function 'insnp_new': inputNew.c:408:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 408 | strncpy(gtype2, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c:406:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 406 | strncpy(gtype1, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c:404:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 404 | strncpy(gtype1, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c:401:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 401 | strncpy(cscore, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c:398:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 398 | strncpy(snpid, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ inputNew.c:395:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation] 395 | strncpy(sampid, field, MAX_FLD-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c input_unsorted.c -o input_unsorted.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ld_graphic_eps.c -o ld_graphic_eps.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ld_with.c -o ld_with.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c mla.c -o mla.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c outdata.c -o outdata.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c pairwise_linkage.c -o pairwise_linkage.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c read_chiamo.c -o read_chiamo.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c read_hapmap.c -o read_hapmap.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c read_pedfile.c -o read_pedfile.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c read_signals.c -o read_signals.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c readped.c -o readped.o readped.c: In function 'readped': readped.c:233:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=] 233 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi); | ^~ readped.c:233:5: note: 'snprintf' output between 3 and 93 bytes into a destination of size 81 233 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c sdfpw.c -o sdfpw.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c single_snp_tests.c -o single_snp_tests.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c snp_summary.c -o snp_summary.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c snpmpy.c -o snpmpy.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c solve_cubic.c -o solve_cubic.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c solve_quadratic.c -o solve_quadratic.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c structure.c -o structure.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c trees.c -o trees.o trees.c: In function '_tr_init': trees.c:382:6: warning: old-style function definition [-Wold-style-definition] 382 | void _tr_init(s) | ^~~~~~~~ trees.c: In function 'init_block': trees.c:411:12: warning: old-style function definition [-Wold-style-definition] 411 | local void init_block(s) | ^~~~~~~~~~ trees.c: In function 'pqdownheap': trees.c:455:12: warning: old-style function definition [-Wold-style-definition] 455 | local void pqdownheap(s, tree, k) | ^~~~~~~~~~ trees.c: In function 'gen_bitlen': trees.c:490:12: warning: old-style function definition [-Wold-style-definition] 490 | local void gen_bitlen(s, desc) | ^~~~~~~~~~ trees.c: In function 'gen_codes': trees.c:577:12: warning: old-style function definition [-Wold-style-definition] 577 | local void gen_codes (tree, max_code, bl_count) | ^~~~~~~~~ trees.c: In function 'build_tree': trees.c:619:12: warning: old-style function definition [-Wold-style-definition] 619 | local void build_tree(s, desc) | ^~~~~~~~~~ trees.c: In function 'scan_tree': trees.c:707:12: warning: old-style function definition [-Wold-style-definition] 707 | local void scan_tree (s, tree, max_code) | ^~~~~~~~~ trees.c: In function 'send_tree': trees.c:752:12: warning: old-style function definition [-Wold-style-definition] 752 | local void send_tree (s, tree, max_code) | ^~~~~~~~~ trees.c: In function 'build_bl_tree': trees.c:803:11: warning: old-style function definition [-Wold-style-definition] 803 | local int build_bl_tree(s) | ^~~~~~~~~~~~~ trees.c: In function 'send_all_trees': trees.c:838:12: warning: old-style function definition [-Wold-style-definition] 838 | local void send_all_trees(s, lcodes, dcodes, blcodes) | ^~~~~~~~~~~~~~ trees.c: In function '_tr_stored_block': trees.c:867:6: warning: old-style function definition [-Wold-style-definition] 867 | void _tr_stored_block(s, buf, stored_len, eof) | ^~~~~~~~~~~~~~~~ trees.c: In function '_tr_align': trees.c:892:6: warning: old-style function definition [-Wold-style-definition] 892 | void _tr_align(s) | ^~~~~~~~~ trees.c: In function '_tr_flush_block': trees.c:921:6: warning: old-style function definition [-Wold-style-definition] 921 | void _tr_flush_block(s, buf, stored_len, eof) | ^~~~~~~~~~~~~~~ trees.c: In function '_tr_tally': trees.c:1022:5: warning: old-style function definition [-Wold-style-definition] 1022 | int _tr_tally (s, dist, lc) | ^~~~~~~~~ trees.c: In function 'compress_block': trees.c:1072:12: warning: old-style function definition [-Wold-style-definition] 1072 | local void compress_block(s, ltree, dtree) | ^~~~~~~~~~~~~~ trees.c: In function 'set_data_type': trees.c:1126:12: warning: old-style function definition [-Wold-style-definition] 1126 | local void set_data_type(s) | ^~~~~~~~~~~~~ trees.c: In function 'bi_reverse': trees.c:1146:16: warning: old-style function definition [-Wold-style-definition] 1146 | local unsigned bi_reverse(code, len) | ^~~~~~~~~~ trees.c: In function 'bi_flush': trees.c:1161:12: warning: old-style function definition [-Wold-style-definition] 1161 | local void bi_flush(s) | ^~~~~~~~ trees.c: In function 'bi_windup': trees.c:1178:12: warning: old-style function definition [-Wold-style-definition] 1178 | local void bi_windup(s) | ^~~~~~~~~ trees.c: In function 'copy_block': trees.c:1197:12: warning: old-style function definition [-Wold-style-definition] 1197 | local void copy_block(s, buf, len, header) | ^~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c uncompr.c -o uncompr.o uncompr.c: In function 'uncompress': uncompr.c:26:13: warning: old-style function definition [-Wold-style-definition] 26 | int ZEXPORT uncompress (dest, destLen, source, sourceLen) | ^~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c zutil.c -o zutil.o zutil.c: In function 'zError': zutil.c:133:22: warning: old-style function definition [-Wold-style-definition] 133 | const char * ZEXPORT zError(err) | ^~~~~~ zutil.c: In function 'zcalloc': zutil.c:300:8: warning: old-style function definition [-Wold-style-definition] 300 | voidpf zcalloc (opaque, items, size) | ^~~~~~~ zutil.c: In function 'zcfree': zutil.c:310:7: warning: old-style function definition [-Wold-style-definition] 310 | void zcfree (opaque, ptr) | ^~~~~~ gcc -shared -s -static-libgcc -o chopsticks.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/meat/chopsticks.buildbin-libdir/00LOCK-chopsticks/00new/chopsticks/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'chopsticks' as chopsticks_1.73.0.zip * DONE (chopsticks)