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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rtracklayer_1.44.4.tar.gz && rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.44.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rtracklayer_1.44.4.zip && rm rtracklayer_1.44.4.tar.gz rtracklayer_1.44.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1054k 100 1054k 0 0 16.4M 0 --:--:-- --:--:-- --:--:-- 18.3M
install for i386
* installing *source* package 'rtracklayer' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:280:4: warning: 'ans_nhits' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(ans_nhits)[i] = nqhits;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
itemPos, bpt->itemCount, bpt->fileName);
^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: 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:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: 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:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: 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:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: 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:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: 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:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: 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:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: 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:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)result, (long long)size);
^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: 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:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: 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:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: 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:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: 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:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: 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:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)uncompressedSize, zlibErrorMessage(err));
^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)compressedSize, zlibErrorMessage(err));
^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:473:8: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((s = skipLeadingSpaces(s)) == NULL)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
file->sparseFileName, version);
^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
readSize, file->url, startPos, actualSize);
^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: 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:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
url, (long long)size, (long long)maxSize);
^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
static void readAndIgnore(int sd, bits64 size)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
converting help for package 'rtracklayer'
finding HTML links ... done
BEDFile-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BEDFile-class.Rd:136: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BEDFile-class.Rd:207: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
BamFile-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:11: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:12: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:13: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:33: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:46: file link 'filterBam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BamFile-methods.Rd:51: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Bed15TrackLine-class html
BigWigFile html
BigWigSelection-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BigWigSelection-class.Rd:15: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BigWigSelection-class.Rd:37: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BigWigSelection-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
BrowserViewList-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/BrowserViewList-class.Rd:13: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Chain-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/Chain-class.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
FastaFile-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/FastaFile-class.Rd:50: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/FastaFile-class.Rd:51: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/FastaFile-class.Rd:58: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/FastaFile-class.Rd:59: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/FastaFile-class.Rd:63: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
GFFFile-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GFFFile-class.Rd:125: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GFFFile-class.Rd:190: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
GRangesForUCSCGenome html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GRangesForUCSCGenome.Rd:31: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GRangesForUCSCGenome.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GRangesForUCSCGenome.Rd:54: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
GenomicData html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GenomicData.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
GenomicSelection html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GenomicSelection.Rd:7: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GenomicSelection.Rd:26: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/GenomicSelection.Rd:33: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
IntegerRangesList-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names'
Quickload-class html
QuickloadGenome-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/QuickloadGenome-class.Rd:60: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/QuickloadGenome-class.Rd:61: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
RTLFile-class html
TabixFile-methods html
TrackDb-class html
TwoBitFile-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/TwoBitFile-class.Rd:92: file link 'replaceAmbiguities' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/TwoBitFile-class.Rd:116: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
UCSCData-class html
UCSCFile-class html
UCSCSchema-class html
UCSCTableQuery-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/UCSCTableQuery-class.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/UCSCTableQuery-class.Rd:71: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
WIGFile-class html
activeView-methods html
asBED html
asGFF html
basicTrackLine-class html
blocks-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/blocks-methods.Rd:9: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
browseGenome html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browseGenome.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browseGenome.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browseGenome.Rd:21: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browseGenome.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browseGenome.Rd:25: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
browserSession-class html
browserSession-methods html
browserView-class html
browserView-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browserView-methods.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/browserView-methods.Rd:16: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
browserViews-methods html
cpneTrack html
export html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/export.Rd:138: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/export.Rd:148: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
genomeBrowsers html
laySequence-methods html
layTrack-methods html
liftOver html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/liftOver.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
readGFF html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:11: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:69: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:73: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/readGFF.Rd:75: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
targets html
tracks-methods html
ucscGenomes html
ucscSession-class html
ucscTrackLine-class html
ucscTrackModes-class html
ucscTrackModes-methods html
ucscView-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/ucscView-class.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpOgnnTS/R.INSTALL157817e51990/rtracklayer/man/ucscView-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
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
install for x64
* installing *source* package 'rtracklayer' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:280:4: warning: 'ans_nhits' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(ans_nhits)[i] = nqhits;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
itemPos, bpt->itemCount, bpt->fileName);
^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: 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:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: 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:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: 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:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: 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:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: 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:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: 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:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: 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:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)result, (long long)size);
^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: 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:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: 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:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: 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:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: 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:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: 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:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)uncompressedSize, zlibErrorMessage(err));
^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
(long long)compressedSize, zlibErrorMessage(err));
^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)maxAlloc);
^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
(unsigned long long)size, errno);
^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(vpt));
^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
ptrToLL(cmb+1));
^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
file->sparseFileName, version);
^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1111:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
(unsigned long)file, clearBlock,
^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
readSize, file->url, startPos, actualSize);
^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: 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:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
url, (long long)size, (long long)maxSize);
^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
static void readAndIgnore(int sd, bits64 size)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.44.4.zip
* DONE (rtracklayer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rtracklayer' successfully unpacked and MD5 sums checked
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rtracklayer.Rcheck/tests_i386/rtracklayer_unit_tests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Wed Oct 16 06:54:43 2019
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
There were 14 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
21.76 2.31 38.31
|
rtracklayer.Rcheck/tests_x64/rtracklayer_unit_tests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Wed Oct 16 06:55:13 2019
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
There were 14 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
26.03 1.75 30.26
|
