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Package 441/514HostnameOS / ArchBUILDCHECKBUILD BIN
rtracklayer 1.14.4
Michael Lawrence
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/rtracklayer
Last Changed Rev: 60820 / Revision: 64395
Last Changed Date: 2011-11-23 08:02:43 -0800 (Wed, 23 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ ERROR ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: rtracklayer
Version: 1.14.4
Command: rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.14.4.tar.gz >rtracklayer-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.14.4.tar.gz && mv rtracklayer.buildbin-libdir/* rtracklayer.Rcheck/ && rmdir rtracklayer.buildbin-libdir
StartedAt: 2012-03-24 02:50:42 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:54:41 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 238.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: rtracklayer.Rcheck
Warnings: NA

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/rtracklayer.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.14.4'
* 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 whether package 'rtracklayer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  cpneTrack.rda    769Kb    591Kb       xz
  targets.rda      147Kb     58Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'D:/biocbld/bbs-2.9-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386/rtracklayer.dll':
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call functions 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 examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'rtracklayer-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BigWigFile-class
> ### Title: BigWigFile objects
> ### Aliases: class:BigWigFile BigWigFile-class BigWigFile
> ###   seqinfo,BigWigFile-method import.bw,BigWigFile-method
> ###   summary,BigWigFile-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> bwf <- BigWigFile(system.file("tests", "test.bw", package = "rtracklayer"))
> seqinfo(bwf)
Warning in seqinfo(bwf) :
  Invalid argument
lseek(5, 184, invalid 'whence' value (1880910261)) failed
Error in seqinfo(bwf) : UCSC library operation failed
Calls: seqinfo -> seqinfo -> .Call
Execution halted

rtracklayer.Rcheck/00install.out:


install for i386

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

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


** libs
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:115:24: warning: 'header_line' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:100:54: warning: 'block' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:109:12: warning: 'qrc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:105:12: warning: 'trc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: 'qstart' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:96:14: warning: 'tstart' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
twoBit.c: In function 'TwoBitFile_read':
twoBit.c:110:35: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness [-Wpointer-sign]
D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include/IRanges_interface.h:342:6: note: expected 'char *' but argument is of type 'Rbyte *'
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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: At top level:
ucsc/cirTree.c:454:8: warning: return type defaults to 'int' [enabled by default]
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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:2543:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2543:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2543:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2543:3: 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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:133:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:133:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:229:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:229:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:229:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:285:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:285:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:285:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:303:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:303:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:495:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:495:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:495:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:544:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:543:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:644:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:644:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1086:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1110:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1110:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1110:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1436:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:121:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"   -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.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-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-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'
Creating a generic function for 'toString' from package 'base' in package 'rtracklayer'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'rtracklayer.Rnw' 
** testing if installed package can be loaded

add DLL for x64

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

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


** libs
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:115:24: warning: 'header_line' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:100:54: warning: 'block' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:109:12: warning: 'qrc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:105:12: warning: 'trc' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: 'qstart' may be used uninitialized in this function [-Wuninitialized]
chain_io.c:96:14: warning: 'tstart' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:110:35: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness [-Wpointer-sign]
D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include/IRanges_interface.h:342:6: note: expected 'char *' but argument is of type 'Rbyte *'
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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: At top level:
ucsc/cirTree.c:454:8: warning: return type defaults to 'int' [enabled by default]
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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:2543:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2543:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2543:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2543:3: 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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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:133:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:133:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:229:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:229:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:229:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:285:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:285:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:285:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:303:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:303:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:495:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:495:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:495:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:544:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:543:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:644:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:644:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat]
ucsc/udc.c:644:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1085:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1086:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1086:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1110:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1110:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1110:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1110:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1436:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1436:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:121:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/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 R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.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-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.14.4.zip

* DONE (rtracklayer)