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BioC 2.14: INSTALL report for CNEr on moscato2

This page was generated on 2014-10-08 08:56:26 -0700 (Wed, 08 Oct 2014).

Package 167/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.0.0
Ge Tan
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CNEr
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: CNEr
Version: 1.0.0
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/CNEr_1.0.0.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch CNEr_1.0.0.tar.gz && rm CNEr_1.0.0.tar.gz
StartedAt: 2014-10-07 18:52:05 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:53:21 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 76.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/CNEr_1.0.0.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch CNEr_1.0.0.tar.gz && rm CNEr_1.0.0.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'CNEr' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
ceScan.c: In function 'myCeScan':
ceScan.c:865:28: warning: unused variable 'i' [-Wunused-variable]
ceScan.c:865:7: warning: unused variable 'nrCNE' [-Wunused-variable]
ceScan.c:862:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c: In function 'myCeScanFile':
ceScan.c:895:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c: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-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:472:8: warning: 'e' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m32 -shared -s -static-libgcc -o CNEr.dll tmp.def IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/CNEr/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'CNEr' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'bin_ranges_from_coord_range_standard':
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'myReadAxt':
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ceScan.c -o ceScan.o
ceScan.c: In function 'ceScan':
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
ceScan.c: In function 'myCeScan':
ceScan.c:865:28: warning: unused variable 'i' [-Wunused-variable]
ceScan.c:865:7: warning: unused variable 'nrCNE' [-Wunused-variable]
ceScan.c:862:17: warning: unused variable 'CNE' [-Wunused-variable]
ceScan.c: In function 'myCeScanFile':
ceScan.c:895:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat]
ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2442:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2442:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2453:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2453:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2455:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2596:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2620:3: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2620:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat]
ucsc/common.c:2620:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat]
ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'findHeadPolyTMaybeMask':
ucsc/dnautil.c:942:5: warning: variable 'pastPoly' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:32:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c: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-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:93:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:116:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:138:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:2: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:160:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:189:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:317:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:321:14: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:359:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:363:18: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:561:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:703:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function 'validateOption':
ucsc/options.c:49:11: warning: variable 'discardMe' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1049:5: warning: unknown conversion type character 'l' in format [-Wformat]
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -m64 -shared -s -static-libgcc -o CNEr.dll tmp.def IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/CNEr/libs/x64
** testing if installed package can be loaded
* DONE (CNEr)