############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library 'D:/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 "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_rtracklayer.c -o R_init_rtracklayer.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c readGFF.c -o readGFF.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bbiHelper.c -o bbiHelper.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bigWig.c -o bigWig.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] strncpy(keyBuf,item->name, maxBedNameSize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] bits64 extraIndexListEndOffset = 0; ^~~~~~~~~~~~~~~~~~~~~~~ bigBed.c: In function 'BBDFile_query': bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized] switch(typeId[efIndex]) { ^ bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(lengthIndex)[efIndex] = index + 1; ^~~~~~~~~~~~~~~~~~~~ bigBed.c:270:5: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(ans, index++, blocks); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:267:5: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(ans, index++, itemRgb); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:263:5: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(ans, index++, new_IRanges("IRanges", thickStart, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ thickWidth, R_NilValue)); ~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:263:5: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized] bigBed.c:260:5: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(ans, index++, score); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(ans, index++, name); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c chain_io.c -o chain_io.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c twoBit.c -o twoBit.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c handlers.c -o handlers.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils.c -o utils.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/memgfx.c -o ucsc/memgfx.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/aliType.c -o ucsc/aliType.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/binRange.c -o ucsc/binRange.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/htmlColor.c -o ucsc/htmlColor.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] dyStringPrintf(string, "%lld,", array[i]); ^ ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args] dyStringPrintf(string, "%lld,", array[i]); ^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/tokenizer.c -o ucsc/tokenizer.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/asParse.c -o ucsc/asParse.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/basicBed.c -o ucsc/basicBed.o ucsc/basicBed.c: In function 'lmCloneBed': ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] strncpy(newBed->strand, bed->strand, sizeof(bed->strand)); ^ ucsc/basicBed.c: In function 'cloneBed': ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] strncpy(newBed->strand, bed->strand, sizeof(bed->strand)); ^ ucsc/basicBed.c: In function 'loadAndValidateBedExt': ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] 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); ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %I64d ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args] 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] strncpy(dupe, itemRgb, sizeof(dupe)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/bigBed.c -o ucsc/bigBed.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] 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=] 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=] errAbort("Item index %lld greater than item count %lld in %s", ~^ %I64d itemPos, bpt->itemCount, bpt->fileName); ~~~~~~~ ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("Item index %lld greater than item count %lld in %s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] bzero(summary, summarySize * sizeof(summary[0])); ^~~~~ ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero' "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] char *blockPt, *blockEnd; ^~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] 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] 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=] 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] 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=] 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=] 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=] errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); ~^ ~~~~~~~~~~~~~~~~ %I64d ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=] errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__); ~^ ~~~~~~~~~~~~~~~~~ %I64d ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf); ~^ ~~~~~~~~~~~~~~~ %I64u ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf); ~^ ~~~~~~~~~~~~~~~ %I64d ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args] verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] 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=] errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file))); ~^ ~~~~~~~~~~~~~~~ %I64d ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file))); ~^ ~~~~~~~~~~~~~~~ %I64d ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args] 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=] errAbort("End of file reading %lld bytes", (long long)size); ^ ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args] 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=] errnoAbort("Error reading %lld bytes", (long long)size); ^ ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args] errnoAbort("Error reading %lld bytes", (long long)size); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] 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] 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=] 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=] 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] 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=] 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=] errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, ~^ ~~~~~~~~~~~~~~~~~ %I64d ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=] errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset, ~^ %s ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] 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] 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=] 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=] 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] 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=] 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=] 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] 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=] 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=] 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] 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=] 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=] 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] errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/dnaseq.c -o ucsc/dnaseq.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/dnautil.c -o ucsc/dnautil.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid)); ^ ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args] safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid)); ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/hash.c -o ucsc/hash.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] 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] 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] static char * headerBytes(char *fileName, int numbytes) ^~~~~~~~~~~ ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function] static char **getDecompressor(char *fileName) ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] errAbort("Couldn't allocate %lld bytes", (long long)fullSize); ^ ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("Couldn't allocate %lld bytes", (long long)fullSize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/sqlNum.c -o ucsc/sqlNum.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] 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=] errAbort("Couldn't zCompress %lld bytes: %s", ~^ %I64d (long long)uncompressedSize, zlibErrorMessage(err)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] errAbort("Couldn't zUncompress %lld bytes: %s", ~^ %I64d (long long)compressedSize, zlibErrorMessage(err)); ~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("Couldn't zUncompress %lld bytes: %s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/dystring.c -o ucsc/dystring.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/hmmstats.c -o ucsc/hmmstats.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/obscure.c -o ucsc/obscure.o ucsc/obscure.c: In function 'sprintLongWithCommas': ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^ ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^ ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^ ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l); ^~~~~~~~~~~~~~~~~~~~ ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld", thousands, l); ^ ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld", thousands, l); ^ ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld", thousands, l); ^~~~~~~~~~~~~ ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld", thousands, l); ^ ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld,%03lld", thousands, l); ^ ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld,%03lld", thousands, l); ^~~~~~~~~~~~~ ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld", l); ^ ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld", l); ^~~~~~ ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=] sprintf(s, "%lld", l); ^ ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args] sprintf(s, "%lld", l); ^~~~~~ 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=] fprintf(stderr, "# pid=%d: %s\n", pid, line); ~^ ~~~ %I64d 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=] fprintf(stderr, "# pid=%d: %s\n", pid, line); ~^ ~~~ %I64d "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/pipeline.c -o ucsc/pipeline.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/rangeTree.c -o ucsc/rangeTree.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/rbTree.c -o ucsc/rbTree.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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=] errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n", ~^ %I64d (unsigned long long)size, errno); ~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args] 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=] errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n", ~^ %I64d (unsigned long long)size, errno); ~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n", ~^ %I64d (unsigned long long)size, errno); ~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n", ~^ %I64d (unsigned long long)size, errno); ~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args] 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=] errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", ^ ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("needMem: trying to allocate %llu bytes (limit: %llu)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n", ~^ %I64d (unsigned long long)size, errno); ~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args] 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=] errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, ^ ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args] errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=] 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] 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=] 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] 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=] 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] safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/dlist.c -o ucsc/dlist.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/hex.c -o ucsc/hex.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/filePath.c -o ucsc/filePath.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/htmlPage.c -o ucsc/htmlPage.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] /* 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=] errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total); ^ ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args] errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=] 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=] 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] 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=] 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=] verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url); ~^ ~~~~~~ %I64d ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args] 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=] 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] 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=] 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=] verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url); ~^ ~~~~~~ %I64d ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args] 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=] 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] 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=] 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=] errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d", ~^ %I64d fd, file->bitmapFileName, offset, udcBitmapHeaderSize); ~~~~~~ ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args] 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=] 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=] 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=] 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=] 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=] verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " ~^ %I64d ucsc/udc.c:879:3: bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size, ~~~~~~~~~~~~~~~~~~ ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=] verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:879:23: bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c:878:17: note: format string is defined here "new version %d\n", ~^ %I64d ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args] 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 'udcCheckCacheBits': ucsc/udc.c:1411:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] (unsigned long)file, clearBlock, ^ ucsc/udc.c:1410:52: warning: unknown conversion type character 'l' in format [-Wformat=] warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", ^ ucsc/udc.c:1410:58: warning: unknown conversion type character 'l' in format [-Wformat=] warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", ^ ucsc/udc.c:1410:10: warning: too many arguments for format [-Wformat-extra-args] warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'fetchMissingBlocks': ucsc/udc.c:1435:30: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", ^ ucsc/udc.c:1435:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=] errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", ~^ %I64d readSize, file->url, startPos, actualSize); ~~~~~~~~ ucsc/udc.c:1435:50: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", ^ ucsc/udc.c:1435:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=] errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", ~^ %s readSize, file->url, startPos, actualSize); ~~~~~~~~~ ucsc/udc.c:1435:11: warning: too many arguments for format [-Wformat-extra-args] errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/udc.c: In function 'udcMustRead': ucsc/udc.c:1678:35: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); ^ ucsc/udc.c:1678:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=] errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); ~^ ~~~~ %I64d ucsc/udc.c:1678:64: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead); ^ ucsc/udc.c:1678:14: warning: too many arguments for format [-Wformat-extra-args] 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:1818:23: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld", ^ ucsc/udc.c:1818:68: warning: unknown conversion type character 'l' in format [-Wformat=] errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld", ^ ucsc/udc.c:1818:14: warning: too many arguments for format [-Wformat-extra-args] 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] static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size) ^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/net.c -o ucsc/net.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/bits.c -o ucsc/bits.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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] /* Use byteRange as a work-around alternate method to get file size (content-length). "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/internet.c -o ucsc/internet.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/https.c -o ucsc/https.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/base64.c -o ucsc/base64.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/verbose.c -o ucsc/verbose.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/os.c -o ucsc/os.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/wildcmp.c -o ucsc/wildcmp.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ucsc/_portimpl.c -o ucsc/_portimpl.o C:/rtools40/mingw64/bin/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 -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/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 converting help for package 'rtracklayer' finding HTML links ... done BEDFile-class html BamFile-methods html Bed15TrackLine-class html BigBedFile html finding level-2 HTML links ... done BigBedSelection html BigWigFile html BigWigSelection-class html BrowserViewList-class html Chain-class html FastaFile-class html GFFFile-class html GRangesForUCSCGenome html GenomicData html GenomicSelection html IntegerRangesList-methods html Quickload-class html QuickloadGenome-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rtracklayer/00new/rtracklayer/help/quickload.html TabixFile-methods html TrackDb-class html TrackHub-class html TrackHubGenome-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rtracklayer/00new/rtracklayer/help/trackhub.html TwoBitFile-class html UCSCData-class html UCSCFile-class html UCSCSchema-class html UCSCTableQuery-class html WIGFile-class html activeView-methods html asBED html asGFF html basicTrackLine-class html blocks-methods html browseGenome html browserSession-class html browserSession-methods html browserView-class html browserView-methods html browserViews-methods html cpneTrack html genomeBrowsers html laySequence-methods html layTrack-methods html liftOver html readGFF html targets html tracks-methods html ucscGenomes html ucscSession-class html ucscTrackLine-class html ucscTrackModes-class html ucscTrackModes-methods html ucscView-class html wigToBigWig html wigTrackLine-class html ** 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) Making 'packages.html' ... done