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BioC 2.13: CHECK report for rtracklayer on moscato1

This page was generated on 2014-04-05 09:49:40 -0700 (Sat, 05 Apr 2014).

Package 634/750HostnameOS / ArchBUILDCHECKBUILD BIN
rtracklayer 1.22.7
Michael Lawrence
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rtracklayer
Last Changed Rev: 88096 / Revision: 88450
Last Changed Date: 2014-03-28 10:08:23 -0700 (Fri, 28 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: rtracklayer
Version: 1.22.7
Command: rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.22.7.tar.gz >rtracklayer-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.22.7.tar.gz && mv rtracklayer.buildbin-libdir/* rtracklayer.Rcheck/ && rmdir rtracklayer.buildbin-libdir
StartedAt: 2014-04-05 06:36:25 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:44:46 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 500.7 seconds
RetCode: 0
Status:  OK  
CheckDir: rtracklayer.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.22.7'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rtracklayer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'GenomicRanges'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'XVector'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::labeledLine' 'BiocGenerics:::testPackage'
  'GenomicRanges:::INVALID.GR.COLNAMES' 'IRanges:::newList'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386/rtracklayer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64/rtracklayer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'rtracklayer.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [25s] OK
** running examples for arch 'x64' ... [23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'rtracklayer_unit_tests.R' [73s]
 [73s] OK
** running tests for arch 'x64'
  Running 'rtracklayer_unit_tests.R' [82s]
 [83s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.

rtracklayer.Rcheck/00install.out:


install for i386

* installing *source* package 'rtracklayer' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:116:24: warning: 'header_line' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:101:54: warning: 'block' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:110:12: warning: 'qrc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:106:12: warning: 'trc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:98:14: warning: 'qstart' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: 'tstart' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
twoBit.c: In function 'TwoBitFile_read':
twoBit.c:111:37: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness [-Wpointer-sign]
D:/biocbld/bbs-2.13-bioc/R/library/XVector/include/XVector_interface.h:81:6: note: expected 'char *' but argument is of type 'Rbyte *'
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_STRSXP_collapse':
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:590:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
ucsc/bbiRead.c:590:1: warning: incompatible implicit declaration of built-in function 'bzero' [enabled by default]
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:703:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:186:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:497:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:497:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:497:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2370:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2370:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2370:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2381:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2381:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2381:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2383:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2383:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2521:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2521:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2523:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2543:17: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2543:17: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2543:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2543:17: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2668:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3134:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3157:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3166:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:943:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:49:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:49:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:49:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:70:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:70:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:70:6: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:559:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:559:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:559:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:562:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:562:5: 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 [-Wuninitialized]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
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]
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]
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]
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]
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]
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]
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]
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:318:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:318:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:322:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:322:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:360:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:360:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:364:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:364:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:139:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:139:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:144:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:144:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:144:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:235:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:235:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:235:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:242:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:242:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:291:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:291:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:291:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:309:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:309:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:501:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:501:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:501:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:550:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:549:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:650:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:650:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1096:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1096:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1096:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1120:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1120:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1120:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1120:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1120:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1446:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1446:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1446:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:127:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m32 -shared -s -static-libgcc -o rtracklayer.dll tmp.def IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.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 -LD:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -pthread -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386
** R
** data
** demo
** inst
** preparing 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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rtracklayer' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:116:24: warning: 'header_line' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:101:54: warning: 'block' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:110:12: warning: 'qrc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:106:12: warning: 'trc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:98:14: warning: 'qstart' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: 'tstart' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
twoBit.c: In function 'TwoBitFile_read':
twoBit.c:111:37: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness [-Wpointer-sign]
D:/biocbld/bbs-2.13-bioc/R/library/XVector/include/XVector_interface.h:81:6: note: expected 'char *' but argument is of type 'Rbyte *'
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_STRSXP_collapse':
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:590:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
ucsc/bbiRead.c:590:1: warning: incompatible implicit declaration of built-in function 'bzero' [enabled by default]
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:703:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:186:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:497:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:497:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:497:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2370:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2370:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2370:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2381:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2381:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2381:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2383:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2383:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2521:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2521:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2523:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2523:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2543:17: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2543:17: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2543:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2543:17: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2668:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2668:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3134:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3134:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3157:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3157:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3166:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3166:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:943:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:49:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:49:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:49:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:70:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:70:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:70:6: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:545:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:553:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:559:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:559:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:559:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:562:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:562:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:704:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
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]
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]
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]
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]
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]
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]
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]
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:318:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:318:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:322:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:322:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:360:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:360:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:364:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:364:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:139:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:139:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:144:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:144:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:144:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:235:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:235:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:235:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:242:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:242:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:291:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:291:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:291:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:309:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:309:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:501:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:501:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:501:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:550:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:549:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:650:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:650:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat]
ucsc/udc.c:650:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1095:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ucsc/udc.c:1096:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1096:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1096:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1120:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1120:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1120:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1120:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1120:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1446:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1446:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1446:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:127:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m64 -shared -s -static-libgcc -o rtracklayer.dll tmp.def IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.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 -LD:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -pthread -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.22.7.zip
* DONE (rtracklayer)

rtracklayer.Rcheck/examples_i386/rtracklayer-Ex.timings:

nameusersystemelapsed
BEDFile-class3.530.274.27
BamFile-methods0.220.010.24
BigWigFile0.210.000.21
BigWigSelection-class0.040.000.04
GFFFile-class3.260.003.26
GenomicSelection0.110.000.11
Quickload-class0.050.000.05
QuickloadGenome-class0.060.000.06
RangedData-methods0.580.000.58
TwoBitFile-class0.140.000.14
UCSCSchema-class0.020.000.02
UCSCTableQuery-class0.010.000.01
WIGFile-class2.810.033.22
asBED000
asGFF0.020.000.01
browseGenome0.010.000.02
browserView-methods000
browserViews-methods000
cpneTrack1.300.021.31
export0.440.000.44
layTrack-methods0.030.000.03
liftOver0.010.000.01
targets0.150.000.15
ucscGenomes0.430.110.74
ucscTrackModes-methods0.030.000.03

rtracklayer.Rcheck/examples_x64/rtracklayer-Ex.timings:

nameusersystemelapsed
BEDFile-class3.700.354.12
BamFile-methods0.310.020.32
BigWigFile000
BigWigSelection-class0.050.000.04
GFFFile-class2.820.002.83
GenomicSelection0.110.000.11
Quickload-class0.060.000.06
QuickloadGenome-class0.080.000.08
RangedData-methods0.650.000.66
TwoBitFile-class0.140.020.15
UCSCSchema-class000
UCSCTableQuery-class0.010.000.01
WIGFile-class2.260.012.28
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods0.020.000.01
cpneTrack1.340.001.34
export0.530.020.55
layTrack-methods0.010.000.02
liftOver0.020.000.01
targets0.090.000.09
ucscGenomes0.470.090.65
ucscTrackModes-methods0.030.000.03