Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for rtracklayer on moscato2

This page was generated on 2015-10-09 09:28:15 -0700 (Fri, 09 Oct 2015).

Package 861/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.28.10
Michael Lawrence
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/rtracklayer
Last Changed Rev: 108005 / Revision: 109384
Last Changed Date: 2015-09-01 12:48:52 -0700 (Tue, 01 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: rtracklayer
Version: 1.28.10
Command: rm -rf rtracklayer.buildbin-libdir rtracklayer.Rcheck && mkdir rtracklayer.buildbin-libdir rtracklayer.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.28.10.tar.gz >rtracklayer.Rcheck\00install.out 2>&1 && cp rtracklayer.Rcheck\00install.out rtracklayer-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.28.10.tar.gz
StartedAt: 2015-10-09 05:54:45 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:00:49 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 363.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: rtracklayer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rtracklayer.buildbin-libdir rtracklayer.Rcheck && mkdir rtracklayer.buildbin-libdir rtracklayer.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.28.10.tar.gz >rtracklayer.Rcheck\00install.out 2>&1 && cp rtracklayer.Rcheck\00install.out rtracklayer-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=rtracklayer.buildbin-libdir --install="check:rtracklayer-install.out" --force-multiarch --no-vignettes --timings rtracklayer_1.28.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/rtracklayer.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.28.10'
* 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 ... WARNING
Found the following significant warnings:
  ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1113:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'E:/biocbld/bbs-3.1-bioc/meat/rtracklayer.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::labeledLine' 'BiocGenerics:::testPackage'
  'GenomicRanges:::INVALID.GR.COLNAMES'
  'S4Vectors:::make_XYZxyz_to_XxYyZz_subscript'
  'S4Vectors:::new_SimpleList_from_list'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import,BEDFile-ANY-ANY : .local: warning in rgb(cols[1, ], cols[2, ],
  cols[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
export,GenomicRanges-GFFFile-ANY : .local: no visible global function
  definition for 'package.version'
getSeq,TwoBitFile : .local: no visible binding for global variable
  'con'
intersectTrack<-,UCSCTableQuery : .local: possible error in
  normArgTrack(value, x, TRUE): unused argument (TRUE)
* 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 GNU extensions in Makefiles ... 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 'E:/biocbld/bbs-3.1-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)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'E:/biocbld/bbs-3.1-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)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [15s] OK
** running examples for arch 'x64' ... [19s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'rtracklayer_unit_tests.R' [21s]
 [21s] OK
** running tests for arch 'x64' ...
  Running 'rtracklayer_unit_tests.R' [27s]
 [27s] 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
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.

rtracklayer.Rcheck/00install.out:


install for i386

* installing *source* package 'rtracklayer' ...
** libs
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataStart':
ucsc/bPlusTree.c:286:12: warning: variable 'childCount' set but not used [-Wunused-but-set-variable]
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/bPlusTree.c:310:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero' [enabled by default]
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:748:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:748:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:748:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:238:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:2476:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'reverseComplementSlashSeparated':
ucsc/dnautil.c:496:5: warning: implicit declaration of function 'isAllNt' [-Wimplicit-function-declaration]
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:977:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:38:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:52:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:473:8: warning: 'e' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:326:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:138:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:570:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:569:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:670:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1138:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1138:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1363:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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 S4Vectors_stubs.o 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 -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -pthread -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'rtracklayer' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c bigWig.c -o bigWig.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c twoBit.c -o twoBit.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c handlers.c -o handlers.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataStart':
ucsc/bPlusTree.c:286:12: warning: variable 'childCount' set but not used [-Wunused-but-set-variable]
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/bPlusTree.c:310:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/bPlusTree.c:310:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/bPlusTree.c:310:2: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero' [enabled by default]
ucsc/bbiRead.c: In function 'bbiTotalSummary':
ucsc/bbiRead.c:748:34: warning: variable 'chromEnd' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:748:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:748:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:238:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:2476:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'reverseComplementSlashSeparated':
ucsc/dnautil.c:496:5: warning: implicit declaration of function 'isAllNt' [-Wimplicit-function-declaration]
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:977:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:38:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:52:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:326:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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:138:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcBitmapOpen':
ucsc/udc.c:570:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable]
ucsc/udc.c:569:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:670:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:670:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat]
ucsc/udc.c:670:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1113:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1114:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1114:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1138:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1138:4: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1138:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat]
ucsc/udc.c:1138:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1363:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/udc.c:1363:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1363:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1499:6: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/udc.c:1499:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/net.c -o ucsc/net.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/internet.c -o ucsc/internet.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/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 S4Vectors_stubs.o 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 -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -pthread -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.28.10.zip
* DONE (rtracklayer)

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

nameusersystemelapsed
BEDFile-class2.040.222.28
BamFile-methods0.170.000.17
BigWigFile000
BigWigSelection-class0.030.000.03
GFFFile-class1.860.011.88
GenomicSelection0.170.020.18
Quickload-class1.610.011.91
QuickloadGenome-class0.20.00.2
RangedData-methods0.200.040.23
TwoBitFile-class0.060.000.07
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class1.020.001.01
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.530.010.55
export0.060.000.06
layTrack-methods000
liftOver000
targets0.060.020.08
ucscGenomes0.110.000.31
ucscTrackModes-methods0.050.000.04

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

nameusersystemelapsed
BEDFile-class2.340.173.02
BamFile-methods0.160.020.17
BigWigFile000
BigWigSelection-class0.030.000.03
GFFFile-class2.200.023.11
GenomicSelection0.180.030.21
Quickload-class2.110.012.13
QuickloadGenome-class0.20.00.2
RangedData-methods0.220.020.24
TwoBitFile-class0.060.000.06
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class1.220.001.22
asBED000
asGFF0.000.010.00
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.460.040.50
export0.070.000.06
layTrack-methods000
liftOver000
targets0.040.010.07
ucscGenomes0.120.000.24
ucscTrackModes-methods0.050.000.04