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BioC 3.5: INSTALL report for CNEr on tokay2

This page was generated on 2017-10-18 14:23:12 -0400 (Wed, 18 Oct 2017).

Package 244/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.12.1
Ge Tan
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CNEr
Branch: RELEASE_3_5
Last Commit: 90d611f
Last Changed Date: 2017-07-09 14:57:38 -0400 (Sun, 09 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.12.1
Command: rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/CNEr_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=CNEr.buildbin-libdir --merge-multiarch CNEr_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL CNEr_1.12.1.zip && rm CNEr_1.12.1.tar.gz CNEr_1.12.1.zip
StartedAt: 2017-10-17 18:35:50 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 18:38:13 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 143.3 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/CNEr_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=CNEr.buildbin-libdir --merge-multiarch CNEr_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL CNEr_1.12.1.zip  && rm CNEr_1.12.1.tar.gz CNEr_1.12.1.zip
###
##############################################################################
##############################################################################


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100 9009k  100 9009k    0     0  57.9M      0 --:--:-- --:--:-- --:--:-- 58.6M

install for i386

* installing *source* package 'CNEr' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   int _binNextShift = binNextShift();
       ^
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
   int _binFirstShift = binFirstShift();
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   struct axt *axt=NULL, *curAxt;
                          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   char rest, path[PATH_LEN];
        ^
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
   int i, n;
          ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE, *nextCNE, *el_CNE;
                 ^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                       ^
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
                            ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
       ^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE;
                 ^
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
   int nrThresholds = GET_LENGTH(winSize);
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
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=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
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=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
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]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
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=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
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=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
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=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
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=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
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=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
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=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
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=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
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=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
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=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
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=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
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]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'fdReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2842:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 int pastPoly = 0;
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
  (unsigned long long)size, errno);
  ^
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=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
              ptrToLL(vpt));
              ^
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=]
              ptrToLL(vpt));
              ^
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=]
                  ptrToLL(cmb+1));
                  ^
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=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
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=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
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=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
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=]
     sprintf(s, "%lld", l);
     ^
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 [-Wmaybe-uninitialized]
     if ((s = skipLeadingSpaces(s)) == NULL)
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 long long discardMe = 0;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     dyStringPrintf(string, "%lld,", array[i]);
     ^
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O3 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o 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 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNEr.buildbin-libdir/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 *source* package 'CNEr' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_CNEr.c -o R_init_CNEr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   int _binNextShift = binNextShift();
       ^
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
   int _binFirstShift = binFirstShift();
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   struct axt *axt=NULL, *curAxt;
                          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
   char rest, path[PATH_LEN];
        ^
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
   int i, n;
          ^
ceScan.c: In function 'freeSlThreshold':
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE, *nextCNE, *el_CNE;
                 ^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                       ^
ceScan.c: In function 'myCeScan':
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
                            ^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
   int nrCNE[nrThresholds], i;
       ^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
   struct slCNE *CNE;
                 ^
ceScan.c: In function 'myCeScanFile':
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
   int nrThresholds = GET_LENGTH(winSize);
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/axt.c -o ucsc/axt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/binRange.c -o ucsc/binRange.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/chain.c -o ucsc/chain.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
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=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
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=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
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]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
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=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
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=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
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=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
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=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
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=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
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=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
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=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
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=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
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=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
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=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
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]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2843:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2844:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2845:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2976:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[0] = u.bytes[7];
                     ^
ucsc/common.c:2977:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[1] = u.bytes[6];
                     ^
ucsc/common.c:2978:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[2] = u.bytes[5];
                     ^
ucsc/common.c:2979:21: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[3] = u.bytes[4];
                     ^
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
        ^
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
        ^
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
        ^
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 int pastPoly = 0;
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/errabort.c -o ucsc/errabort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/intExp.c -o ucsc/intExp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/kxTok.c -o ucsc/kxTok.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:100:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
  (unsigned long long)size, errno);
  ^
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=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
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=]
              (unsigned long long)size, errno);
              ^
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=]
              ptrToLL(vpt));
              ^
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=]
              ptrToLL(vpt));
              ^
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=]
                  ptrToLL(cmb+1));
                  ^
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=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
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=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
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=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
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=]
     sprintf(s, "%lld", l);
     ^
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=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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]
 long long discardMe = 0;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/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=]
     dyStringPrintf(string, "%lld,", array[i]);
     ^
ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include"   -I"C:/local323/include"  -g   -O2 -Wall  -std=gnu99 -mtune=core2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNEr.dll tmp.def S4Vectors_stubs.o 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 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.12.1.zip
* DONE (CNEr)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'CNEr' successfully unpacked and MD5 sums checked