##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.48.0.tar.gz
###
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install for i386
* installing *source* package 'rtracklayer' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
~^
%I64d
itemPos, bpt->itemCount, bpt->fileName);
~~~~~~~
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Item index %lld greater than item count %lld in %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
bzero(summary, summarySize * sizeof(summary[0]));
^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
~^
%I64d
(long long)uncompressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zCompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
~^
%I64d
(long long)compressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zUncompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:138:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:143:43: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:49: 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:234:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:241:57: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:241:10: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:54: 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:290:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:290:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:308:53: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:308:7: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:515:42: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^
ucsc/udc.c:515:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
~^
%I64d
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
~~~~~~
ucsc/udc.c:515:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:665:40: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:48: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:56: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:64: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
~^
%I64d
ucsc/udc.c:667:3:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~
ucsc/udc.c:665:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:667:23:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:666:17: note: format string is defined here
"new version %d\n",
~^
%I64d
ucsc/udc.c:665:13: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1110:52: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1110:58: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1110:10: warning: too many arguments for format [-Wformat-extra-args]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1135:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1135:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%I64d
readSize, file->url, startPos, actualSize);
~~~~~~~~
ucsc/udc.c:1135:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1135:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%s
readSize, file->url, startPos, actualSize);
~~~~~~~~~
ucsc/udc.c:1135:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1361:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
~^ ~~~~
%I64d
ucsc/udc.c:1361:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1361:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1496:23: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1496:68: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1496:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
static void readAndIgnore(int sd, bits64 size)
^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw32/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-3.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/BEDFile-class.Rd:210: 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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names'
Quickload-class html
QuickloadGenome-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/browseGenome.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/browseGenome.Rd:20: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/browseGenome.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/browseGenome.Rd:24: 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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/export.Rd:137: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/rtracklayer/man/export.Rd:147: 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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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-3.11-bioc/tmpdir/RtmpWouxFA/R.INSTALL179cef75ac2/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:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
~^
%I64d
itemPos, bpt->itemCount, bpt->fileName);
~~~~~~~
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Item index %lld greater than item count %lld in %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
bzero(summary, summarySize * sizeof(summary[0]));
^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
~^
%I64d
(long long)uncompressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zCompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
~^
%I64d
(long long)compressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zUncompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
ucsc/obscure.c:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:138:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:143:43: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:143:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:49: 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:234:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:234:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:241:57: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:241:10: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:54: 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:290:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:290:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:308:53: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:308:7: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:515:42: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^
ucsc/udc.c:515:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
~^
%I64d
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
~~~~~~
ucsc/udc.c:515:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:665:40: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:48: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:56: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:64: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^
ucsc/udc.c:665:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
~^
%I64d
ucsc/udc.c:667:3:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~
ucsc/udc.c:665:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:667:23:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:666:17: note: format string is defined here
"new version %d\n",
~^
%I64d
ucsc/udc.c:665:13: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:1110:52: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1110:58: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1110:10: warning: too many arguments for format [-Wformat-extra-args]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1135:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1135:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%I64d
readSize, file->url, startPos, actualSize);
~~~~~~~~
ucsc/udc.c:1135:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1135:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%s
readSize, file->url, startPos, actualSize);
~~~~~~~~~
ucsc/udc.c:1135:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1361:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
~^ ~~~~
%I64d
ucsc/udc.c:1361:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1361:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1496:23: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1496:68: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1496:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
static void readAndIgnore(int sd, bits64 size)
^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o 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-3.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.48.0.zip
* DONE (rtracklayer)
