############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'rtracklayer' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bbiHelper.c -o bbiHelper.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBedHelper.c -o bigBedHelper.o bigBedHelper.c: In function 'bbNamedFileChunkKey': bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation] 148 | strncpy(keyBuf,item->name, maxBedNameSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBed.c -o bigBed.o bigBed.c: In function 'BBDFile_write': bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable] 338 | bits64 extraIndexListEndOffset = 0; | ^~~~~~~~~~~~~~~~~~~~~~~ bigBed.c: In function 'BBDFile_query': bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized] 226 | switch(typeId[efIndex]) { | ^ bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] 236 | INTEGER(lengthIndex)[efIndex] = index + 1; | ^~~~~~~~~~~~~~~~~~~~ bigBed.c:218:7: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] 218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:209:7: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized] 209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:204:7: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized] 204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:205:7: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized] 205 | INTEGER(thickStart)[i] = bed->thickStart; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:198:7: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized] 198 | INTEGER(score)[i] = bed->score; | ^~~~~~~~~~~~~~ bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized] 257 | SET_VECTOR_ELT(ans, index++, name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memgfx.c -o ucsc/memgfx.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/aliType.c -o ucsc/aliType.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlColor.c -o ucsc/htmlColor.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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:1041:31: warning: unknown conversion type character 'l' in format [-Wformat=] 1041 | dyStringPrintf(string, "%lld,", array[i]); | ^ ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args] 1041 | dyStringPrintf(string, "%lld,", array[i]); | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/tokenizer.c -o ucsc/tokenizer.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/asParse.c -o ucsc/asParse.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/basicBed.c -o ucsc/basicBed.o ucsc/basicBed.c: In function 'loadAndValidateBedExt': ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=] 1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name); | ^ ucsc/basicBed.c:1619:62: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=] 1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * long long unsigned int | %I64d ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args] 1619 | lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/basicBed.c: In function 'bedParseRgb': ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation] 997 | strncpy(dupe, itemRgb, sizeof(dupe)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bigBed.c -o ucsc/bigBed.o ucsc/bigBed.c: In function 'extractField': ucsc/bigBed.c:314:2: warning: '%s' directive argument is null [-Wformat-overflow=] 314 | warn("Not enough fields in extractField of %s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o ucsc/bPlusTree.c: In function 'bptDataOffset': ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=] 307 | errAbort("Item index %lld greater than item count %lld in %s", | ^ ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=] 307 | errAbort("Item index %lld greater than item count %lld in %s", | ^ ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=] 307 | errAbort("Item index %lld greater than item count %lld in %s", | ~^ | | | char * | %I64d 308 | itemPos, bpt->itemCount, bpt->fileName); | ~~~~~~~ | | | long long unsigned int ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args] 307 | errAbort("Item index %lld greater than item count %lld in %s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'writeIndexLevel', inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:567:29: ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 461 | keyBuf[keySize] = 0; | ~~~~~~~~~~~~~~~~^~~ ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile': ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here 460 | char keyBuf[keySize+1]; | ^~~~~~ In function 'writeLeafLevel', inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:575:1: ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 513 | keyBuf[keySize] = 0; | ~~~~~~~~~~~~~~~~^~~ ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile': ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here 512 | char keyBuf[keySize+1]; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended': ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration] 635 | bzero(summary, summarySize * sizeof(summary[0])); | ^~~~~ ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero' gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o ucsc/bwgQuery.c: In function 'bigWigIntervalQuery': ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable] 187 | char *blockPt, *blockEnd; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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:238:50: warning: unknown conversion type character 'l' in format [-Wformat=] 238 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount); | ^ ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args] 238 | verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c: In function 'writeTreeToOpenFile': ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=] 319 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]); | ^ ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args] 319 | verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=] 334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^ ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=] 334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^ ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 334 | 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:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=] 334 | 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:334:18: warning: too many arguments for format [-Wformat-extra-args] 334 | errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c: In function 'rFindOverlappingBlocks': ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=] 505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf); | ^ ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] 505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf); | ~^ ~~~~~~~~~~~~~~~ | | | | unsigned int long long unsigned int | %I64u ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args] 505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/cirTree.c: In function 'rEnumerateBlocks': ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=] 585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf); | ^ ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=] 585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf); | ~^ ~~~~~~~~~~~~~~~ | | | | int long long unsigned int | %I64d ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args] 585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=] 2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ^ ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ~^ ~~~~~~~~~~~~~~~ | | | | | long long int | char * | %I64d ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args] 2476 | errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustRead': ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=] 2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ^ ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ~^ ~~~~~~~~~~~~~~~ | | | | | long long int | char * | %I64d ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args] 2487 | errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=] 2489 | errAbort("End of file reading %lld bytes", (long long)size); | ^ ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args] 2489 | errAbort("End of file reading %lld bytes", (long long)size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustReadFd': ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=] 2630 | errnoAbort("Error reading %lld bytes", (long long)size); | ^ ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args] 2630 | errnoAbort("Error reading %lld bytes", (long long)size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=] 2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^ ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=] 2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^ ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args] 2632 | errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustWriteFd': ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=] 2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.", | ^ ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=] 2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.", | ^ ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args] 2647 | errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'mustLseek': ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=] 2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ^ ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=] 2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ~^ ~~~~~~~~~~~~~~~~~ | | | | char * long long int | %I64d ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=] 2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ~^ | | | int | %s 2659 | ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * 2660 | (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args] 2658 | errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'fileOffsetSizeMerge': ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=] 2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^ ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=] 2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^ ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args] 2785 | errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safecpy': ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^ ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=] 3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^ ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args] 3251 | errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safencpy': ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^ ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=] 3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^ ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args] 3260 | errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c: In function 'safecat': ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3276 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen)); | ^ ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=] 3276 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen)); | ^ ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args] 3276 | 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:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=] 3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^ ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=] 3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^ ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args] 3285 | errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o ucsc/errAbort.c: In function 'getThreadVars': ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=] 356 | safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid)); | ^ ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args] 356 | safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid)); | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort': ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=] 1083 | safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit); | ^ ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args] 1083 | safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function] 112 | static char * headerBytes(char *fileName, int numbytes) | ^~~~~~~~~~~ ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function] 35 | static char **getDecompressor(char *fileName) | ^~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o ucsc/zlibFace.c: In function 'zCompress': ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=] 51 | errAbort("Couldn't zCompress %lld bytes: %s", | ^ ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 51 | errAbort("Couldn't zCompress %lld bytes: %s", | ~^ | | | char * | %I64d 52 | (long long)uncompressedSize, zlibErrorMessage(err)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long int ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args] 51 | errAbort("Couldn't zCompress %lld bytes: %s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/zlibFace.c: In function 'zUncompress': ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=] 72 | errAbort("Couldn't zUncompress %lld bytes: %s", | ^ ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=] 72 | errAbort("Couldn't zUncompress %lld bytes: %s", | ~^ | | | char * | %I64d 73 | (long long)compressedSize, zlibErrorMessage(err)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long int ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args] 72 | errAbort("Couldn't zUncompress %lld bytes: %s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=] 789 | 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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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:90:50: warning: unknown conversion type character 'l' in format [-Wformat=] 90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=] 90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args] 90 | errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=] 93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 94 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args] 93 | errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needLargeMemResize': ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=] 113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=] 113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args] 113 | errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=] 116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 117 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args] 116 | errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needHugeMem': ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=] 138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 139 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args] 138 | errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needHugeMemResize': ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=] 160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 161 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args] 160 | errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'needMem': ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=] 186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=] 186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^ ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args] 186 | errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=] 189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ^ ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=] 189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ~^ | | | int | %I64d 190 | (unsigned long long)size, errno); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args] 189 | errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'carefulFree': ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=] 325 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, | ^ ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args] 325 | errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=] 331 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n", | ^ ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args] 331 | errAbort("Bad end cookie %x%x%x%x freeing %llx\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c: In function 'carefulCheckHeap': ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=] 376 | safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie, | ^ ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args] 376 | safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=] 383 | safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n", | ^ ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args] 383 | safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hex.c -o ucsc/hex.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/filePath.c -o ucsc/filePath.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlPage.c -o ucsc/htmlPage.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o In file included from ucsc/udc.c:41: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | ucsc/udc.c: In function 'udcReadAndIgnore': ucsc/udc.c:223:61: warning: unknown conversion type character 'l' in format [-Wformat=] 223 | errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total); | ^ ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args] 223 | errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=] 228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size); | ^ ucsc/udc.c:228:65: warning: unknown conversion type character 'l' in format [-Wformat=] 228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size); | ^ ucsc/udc.c:228:14: warning: too many arguments for format [-Wformat-extra-args] 228 | errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcDataViaLocal': ucsc/udc.c:340:49: warning: unknown conversion type character 'l' in format [-Wformat=] 340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ^ ucsc/udc.c:340:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=] 340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ~^ ~~~~~~ | | | | char * long long unsigned int | %I64d ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args] 340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:347:57: warning: unknown conversion type character 'l' in format [-Wformat=] 347 | warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset); | ^ ucsc/udc.c:347:10: warning: too many arguments for format [-Wformat-extra-args] 347 | warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcDataViaSlow': ucsc/udc.c:396:54: warning: unknown conversion type character 'l' in format [-Wformat=] 396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ^ ucsc/udc.c:396:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=] 396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ~^ ~~~~~~ | | | | char * long long unsigned int | %I64d ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args] 396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:414:53: warning: unknown conversion type character 'l' in format [-Wformat=] 414 | warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset); | ^ ucsc/udc.c:414:7: warning: too many arguments for format [-Wformat-extra-args] 414 | warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse': ucsc/udc.c:721:42: warning: unknown conversion type character 'l' in format [-Wformat=] 721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d", | ^ ucsc/udc.c:721:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=] 721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d", | ~^ | | | int | %I64d 722 | fd, file->bitmapFileName, offset, udcBitmapHeaderSize); | ~~~~~~ | | | long long int ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args] 721 | errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'setInitialCachedDataBounds': ucsc/udc.c:877:40: warning: unknown conversion type character 'l' in format [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^ ucsc/udc.c:877:48: warning: unknown conversion type character 'l' in format [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^ ucsc/udc.c:877:56: warning: unknown conversion type character 'l' in format [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^ ucsc/udc.c:877:64: warning: unknown conversion type character 'l' in format [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^ ucsc/udc.c:877:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ~^ | | | char * | %I64d 878 | "new version %d\n", 879 | bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size, | ~~~~~~~~~~~~~~~~~~ | | | long long unsigned int ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 878 | "new version %d\n", 879 | bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long int ucsc/udc.c:878:17: note: format string is defined here 878 | "new version %d\n", | ~^ | | | int | %I64d ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args] 877 | verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'djb2_hash': ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1088 | while (c = *str++) | ^ ucsc/udc.c: In function 'udcCheckCacheBits': ucsc/udc.c:1446:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1446 | (unsigned long)file, clearBlock, | ^ ucsc/udc.c:1445:52: warning: unknown conversion type character 'l' in format [-Wformat=] 1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", | ^ ucsc/udc.c:1445:58: warning: unknown conversion type character 'l' in format [-Wformat=] 1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", | ^ ucsc/udc.c:1445:10: warning: too many arguments for format [-Wformat-extra-args] 1445 | warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'fetchMissingBlocks': ucsc/udc.c:1470:30: warning: unknown conversion type character 'l' in format [-Wformat=] 1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", | ^ ucsc/udc.c:1470:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=] 1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", | ~^ | | | char * | %I64d 1471 | readSize, file->url, startPos, actualSize); | ~~~~~~~~ | | | long long unsigned int ucsc/udc.c:1470:50: warning: unknown conversion type character 'l' in format [-Wformat=] 1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", | ^ ucsc/udc.c:1470:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=] 1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", | ~^ | | | int | %s 1471 | readSize, file->url, startPos, actualSize); | ~~~~~~~~~ | | | char * ucsc/udc.c:1470:11: warning: too many arguments for format [-Wformat-extra-args] 1470 | errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcMustRead': ucsc/udc.c:1713:35: warning: unknown conversion type character 'l' in format [-Wformat=] 1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); | ^ ucsc/udc.c:1713:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=] 1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); | ~^ ~~~~ | | | | char * long long unsigned int | %I64d ucsc/udc.c:1713:64: warning: unknown conversion type character 'l' in format [-Wformat=] 1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); | ^ ucsc/udc.c:1713:14: warning: too many arguments for format [-Wformat-extra-args] 1713 | errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcFileReadAll': ucsc/udc.c:1853:23: warning: unknown conversion type character 'l' in format [-Wformat=] 1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld", | ^ ucsc/udc.c:1853:68: warning: unknown conversion type character 'l' in format [-Wformat=] 1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld", | ^ ucsc/udc.c:1853:14: warning: too many arguments for format [-Wformat-extra-args] 1853 | errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: ucsc/udc.c:211:13: warning: 'udcReadAndIgnore' defined but not used [-Wunused-function] 211 | static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size) | ^~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o In file included from ucsc/twoBit.c:15: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -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/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -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" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LF:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/x64 ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer' ** 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 * DONE (rtracklayer)