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INSTALL report for rtracklayer on tokay2

This page was generated on 2018-10-17 08:33:47 -0400 (Wed, 17 Oct 2018).

Package 1295/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.40.6
Michael Lawrence
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/rtracklayer
Branch: RELEASE_3_7
Last Commit: ba9a6e7
Last Changed Date: 2018-08-30 18:09:48 -0400 (Thu, 30 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: rtracklayer
Version: 1.40.6
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rtracklayer_1.40.6.tar.gz && rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.40.6.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rtracklayer_1.40.6.zip && rm rtracklayer_1.40.6.tar.gz rtracklayer_1.40.6.zip
StartedAt: 2018-10-16 19:51:00 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:53:57 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 177.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rtracklayer_1.40.6.tar.gz && rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.40.6.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rtracklayer_1.40.6.zip && rm rtracklayer_1.40.6.tar.gz rtracklayer_1.40.6.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1053k  100 1053k    0     0  14.3M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'rtracklayer' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
  ^
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:473:8: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((s = skipLeadingSpaces(s)) == NULL)
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
     ^
ucsc/udc.c:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.buildbin-libdir/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:135: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:201: 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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names'
    Quickload-class                         html  
    QuickloadGenome-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/TwoBitFile-class.Rd:108: 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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:69: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:70: 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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:21: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:25: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    browserSession-class                    html  
    browserSession-methods                  html  
    browserView-class                       html  
    browserView-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:138: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:148: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    genomeBrowsers                          html  
    laySequence-methods                     html  
    layTrack-methods                        html  
    liftOver                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/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-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:43: 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
In R CMD INSTALL

install for x64

* installing *source* package 'rtracklayer' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
  ^
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1111:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   (unsigned long)file, clearBlock,
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
     ^
ucsc/udc.c:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.40.6.zip
* DONE (rtracklayer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'rtracklayer' successfully unpacked and MD5 sums checked
In R CMD INSTALL