############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=CNEr.buildbin-libdir CNEr_1.32.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'CNEr' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_CNEr.c -o R_init_CNEr.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function 'bin_ranges_from_coord_range_standard': utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable] 50 | int _binNextShift = binNextShift(); | ^~~~~~~~~~~~~ utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable] 49 | int _binFirstShift = binFirstShift(); | ^~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o io.c: In function 'myReadAxt': io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable] 94 | struct axt *axt=NULL, *curAxt; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ceScan.c -o ceScan.o ceScan.c: In function 'ceScan': ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable] 615 | char rest, path[PATH_LEN]; | ^~~~ ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable] 613 | int i, n; | ^ ceScan.c: In function 'freeSlThreshold': ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable] 674 | struct slCNE *CNE, *nextCNE, *el_CNE; | ^~~ ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable] 673 | struct slThreshold *thresholds, *nextThreshold, *el_threshold; | ^~~~~~~~~~ ceScan.c: In function 'myCeScan': ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^ ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^~~~~ ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable] 865 | struct slCNE *CNE; | ^~~ ceScan.c: In function 'myCeScanFile': ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable] 898 | int nrThresholds = GET_LENGTH(winSize); | ^~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/axt.c -o ucsc/axt.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/chain.c -o ucsc/chain.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o ucsc/cirTree.c: In function 'rTreeFromChromRangeArray': ucsc/cirTree.c:234:50: warning: unknown conversion type character 'l' in format [-Wformat=] 234 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount); | ^ ucsc/cirTree.c:234:12: warning: too many arguments for format [-Wformat-extra-args] 234 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c: In function 'writeTreeToOpenFile': ucsc/cirTree.c:315:45: warning: unknown conversion type character 'l' in format [-Wformat=] 315 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]); | ^ ucsc/cirTree.c:315:16: warning: too many arguments for format [-Wformat-extra-args] 315 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c:330:54: warning: unknown conversion type character 'l' in format [-Wformat=] 330 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^ ucsc/cirTree.c:330:62: warning: unknown conversion type character 'l' in format [-Wformat=] 330 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^ ucsc/cirTree.c:330:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 330 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long long unsigned int | %I64d ucsc/cirTree.c:330:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=] 330 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ~^ ~~~~~~~~~~~~~~~~~ | | | | char * long long unsigned int | %I64d ucsc/cirTree.c:330:18: warning: too many arguments for format [-Wformat-extra-args] 330 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o ucsc/common.c: In function 'mustWrite': ucsc/common.c:2442:31: warning: unknown conversion type character 'l' in format [-Wformat=] 2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ^ ucsc/common.c:2442:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ~^ ~~~~~~~~~~~~~~~ | | | | | long long int | char * | %I64d ucsc/common.c:2442:14: warning: too many arguments for format [-Wformat-extra-args] 2442 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustRead': ucsc/common.c:2453:28: warning: unknown conversion type character 'l' in format [-Wformat=] 2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ^ ucsc/common.c:2453:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ~^ ~~~~~~~~~~~~~~~ | | | | | long long int | char * | %I64d ucsc/common.c:2453:11: warning: too many arguments for format [-Wformat-extra-args] 2453 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2455:34: warning: unknown conversion type character 'l' in format [-Wformat=] 2455 | errAbort("End of file reading %lld bytes", (long long)size); | ^ ucsc/common.c:2455:11: warning: too many arguments for format [-Wformat-extra-args] 2455 | errAbort("End of file reading %lld bytes", (long long)size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustReadFd': ucsc/common.c:2596:30: warning: unknown conversion type character 'l' in format [-Wformat=] 2596 | errnoAbort("Error reading %lld bytes", (long long)size); | ^ ucsc/common.c:2596:13: warning: too many arguments for format [-Wformat-extra-args] 2596 | errnoAbort("Error reading %lld bytes", (long long)size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2598:34: warning: unknown conversion type character 'l' in format [-Wformat=] 2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^ ucsc/common.c:2598:50: warning: unknown conversion type character 'l' in format [-Wformat=] 2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^ ucsc/common.c:2598:11: warning: too many arguments for format [-Wformat-extra-args] 2598 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustLseek': ucsc/common.c:2618:29: warning: unknown conversion type character 'l' in format [-Wformat=] 2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ^ ucsc/common.c:2618:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=] 2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ~^ ~~~~~~~~~~~~~~~~~ | | | | char * long long int | %I64d ucsc/common.c:2618:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=] 2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ~^ | | | int | %s 2619 | ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * 2620 | (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2618:16: warning: too many arguments for format [-Wformat-extra-args] 2618 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'fileOffsetSizeMerge': ucsc/common.c:2745:60: warning: unknown conversion type character 'l' in format [-Wformat=] 2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^ ucsc/common.c:2745:65: warning: unknown conversion type character 'l' in format [-Wformat=] 2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^ ucsc/common.c:2745:18: warning: too many arguments for format [-Wformat-extra-args] 2745 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safecpy': ucsc/common.c:3211:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^ ucsc/common.c:3211:58: warning: unknown conversion type character 'l' in format [-Wformat=] 3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^ ucsc/common.c:3211:14: warning: too many arguments for format [-Wformat-extra-args] 3211 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safencpy': ucsc/common.c:3220:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^ ucsc/common.c:3220:61: warning: unknown conversion type character 'l' in format [-Wformat=] 3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^ ucsc/common.c:3220:14: warning: too many arguments for format [-Wformat-extra-args] 3220 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safecat': ucsc/common.c:3236:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen)); | ^ ucsc/common.c:3236:62: warning: unknown conversion type character 'l' in format [-Wformat=] 3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen)); | ^ ucsc/common.c:3236:14: warning: too many arguments for format [-Wformat-extra-args] 3236 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safencat': ucsc/common.c:3245:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^ ucsc/common.c:3245:62: warning: unknown conversion type character 'l' in format [-Wformat=] 3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^ ucsc/common.c:3245:14: warning: too many arguments for format [-Wformat-extra-args] 3245 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'byteSwap64': ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2846 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2847 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2848 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2849 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'readBits64': ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2846 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2847 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2848 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2849 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'fdReadBits64': ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2846 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2847 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2848 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2849 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'memReadBits64': ucsc/common.c:2846:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2846 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2847:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2847 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2848:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2848 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2849:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2849 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2840:28: note: while referencing 'bytes' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2840:41: note: defined here 'v' 2840 | union {bits64 whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'byteSwapDouble': ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2980 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2981 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2982 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2983 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'readDouble': ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2980 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2981 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2982 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2983 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c: In function 'memReadDouble': ucsc/common.c:2980:8: warning: array subscript 4 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2980 | v.bytes[4] = u.bytes[3]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2981:8: warning: array subscript 5 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2981 | v.bytes[5] = u.bytes[2]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2982:8: warning: array subscript 6 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2982 | v.bytes[6] = u.bytes[1]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ ucsc/common.c:2983:8: warning: array subscript 7 is above array bounds of 'unsigned char[4]' [-Warray-bounds] 2983 | v.bytes[7] = u.bytes[0]; | ~~~~~~~^~~ ucsc/common.c:2974:28: note: while referencing 'bytes' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^~~~~ ucsc/common.c:2974:41: note: defined here 'v' 2974 | union {double whole; UBYTE bytes[4];} u,v; | ^ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask': ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable] 942 | int pastPoly = 0; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errabort.c -o ucsc/errabort.o ucsc/errabort.c:30:19: warning: 'rcsid' defined but not used [-Wunused-const-variable=] 30 | static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $"; | ^~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/intExp.c -o ucsc/intExp.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/kxTok.c -o ucsc/kxTok.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function] 100 | static char * headerBytes(char *fileName, int numbytes) | ^~~~~~~~~~~ ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function] 32 | static char **getDecompressor(char *fileName) | ^~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o ucsc/localmem.c: In function 'newBlock': ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=] 38 | errAbort("Couldn't allocate %lld bytes", (long long)fullSize); | ^ ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args] 38 | errAbort("Couldn't allocate %lld bytes", (long long)fullSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o ucsc/memalloc.c: In function 'needLargeMem': ucsc/memalloc.c:89:50: warning: unknown conversion type character 'l' in format [-Wformat=] 89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:89:69: warning: unknown conversion type character 'l' in format [-Wformat=] 89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:89:14: warning: too many arguments for format [-Wformat-extra-args] 89 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:92:60: warning: unknown conversion type character 'l' in format [-Wformat=] 92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:92:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 93 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:92:14: warning: too many arguments for format [-Wformat-extra-args] 92 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needLargeMemResize': ucsc/memalloc.c:112:56: warning: unknown conversion type character 'l' in format [-Wformat=] 112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:112:75: warning: unknown conversion type character 'l' in format [-Wformat=] 112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:112:14: warning: too many arguments for format [-Wformat-extra-args] 112 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:115:66: warning: unknown conversion type character 'l' in format [-Wformat=] 115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:115:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 116 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:115:14: warning: too many arguments for format [-Wformat-extra-args] 115 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needHugeMem': ucsc/memalloc.c:137:64: warning: unknown conversion type character 'l' in format [-Wformat=] 137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:137:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 138 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:137:14: warning: too many arguments for format [-Wformat-extra-args] 137 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needHugeMemResize': ucsc/memalloc.c:159:67: warning: unknown conversion type character 'l' in format [-Wformat=] 159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:159:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 160 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:159:14: warning: too many arguments for format [-Wformat-extra-args] 159 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needMem': ucsc/memalloc.c:185:45: warning: unknown conversion type character 'l' in format [-Wformat=] 185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:185:64: warning: unknown conversion type character 'l' in format [-Wformat=] 185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:185:14: warning: too many arguments for format [-Wformat-extra-args] 185 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:188:55: warning: unknown conversion type character 'l' in format [-Wformat=] 188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:188:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 189 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:188:14: warning: too many arguments for format [-Wformat-extra-args] 188 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'carefulFree': ucsc/memalloc.c:316:45: warning: unknown conversion type character 'l' in format [-Wformat=] 316 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, | ^ ucsc/memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args] 316 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:319:49: warning: unknown conversion type character 'l' in format [-Wformat=] 319 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n", | ^ ucsc/memalloc.c:319:14: warning: too many arguments for format [-Wformat-extra-args] 319 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'carefulCheckHeap': ucsc/memalloc.c:358:50: warning: unknown conversion type character 'l' in format [-Wformat=] 358 | errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie, | ^ ucsc/memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args] 358 | errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:361:54: warning: unknown conversion type character 'l' in format [-Wformat=] 361 | errAbort("Bad end cookie %x%x%x%x checking %llx\n", | ^ ucsc/memalloc.c:361:18: warning: too many arguments for format [-Wformat-extra-args] 361 | errAbort("Bad end cookie %x%x%x%x checking %llx\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o ucsc/obscure.c: In function 'printVmPeak': ucsc/obscure.c:703:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=] 703 | fprintf(stderr, "# pid=%d: %s\n", pid, line); | ~^ ~~~ | | | | int pid_t {aka long long int} | %lld gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/options.c -o ucsc/options.o ucsc/options.c: In function 'validateOption': ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable] 49 | long long discardMe = 0; | ^~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o ucsc/sqlList.c: In function 'sqlLongLongArrayToString': ucsc/sqlList.c:1049:31: warning: unknown conversion type character 'l' in format [-Wformat=] 1049 | dyStringPrintf(string, "%lld,", array[i]); | ^ ucsc/sqlList.c:1049:28: warning: too many arguments for format [-Wformat-extra-args] 1049 | dyStringPrintf(string, "%lld,", array[i]); | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -g -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/CNEr/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 'CNEr' as CNEr_1.32.0.zip * DONE (CNEr)