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BioC 3.4: CHECK report for CNEr on moscato1

This page was generated on 2016-09-21 03:45:32 -0700 (Wed, 21 Sep 2016).

Package 221/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.9.39
Ge Tan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNEr
Last Changed Rev: 120860 / Revision: 121152
Last Changed Date: 2016-09-12 07:04:22 -0700 (Mon, 12 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNEr
Version: 1.9.39
Command: rm -rf CNEr.buildbin-libdir CNEr.Rcheck && mkdir CNEr.buildbin-libdir CNEr.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNEr.buildbin-libdir CNEr_1.9.39.tar.gz >CNEr.Rcheck\00install.out 2>&1 && cp CNEr.Rcheck\00install.out CNEr-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CNEr.buildbin-libdir --install="check:CNEr-install.out" --force-multiarch --no-vignettes --timings CNEr_1.9.39.tar.gz
StartedAt: 2016-09-20 05:58:50 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:08:20 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 570.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CNEr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNEr.buildbin-libdir CNEr.Rcheck && mkdir CNEr.buildbin-libdir CNEr.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNEr.buildbin-libdir CNEr_1.9.39.tar.gz >CNEr.Rcheck\00install.out 2>&1 && cp CNEr.Rcheck\00install.out CNEr-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CNEr.buildbin-libdir --install="check:CNEr-install.out" --force-multiarch --no-vignettes --timings CNEr_1.9.39.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/CNEr.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNEr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNEr' version '1.9.39'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNEr' can be installed ... WARNING
Found the following significant warnings:
  ucsc/cirTree.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:315:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:330:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2442:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2453:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2455:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2596:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2598:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2620:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2745:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3211:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3220:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3236:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3245:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:90:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:113:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:160:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:186:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:317:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:321:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:359:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:363:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:544:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:552:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:558:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:561:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/sqlList.c:1049:5: warning: too many arguments for format [-Wformat-extra-args]
See 'D:/biocbld/bbs-3.4-bioc/meat/CNEr.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 17.5Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'S4Vectors:::make_zero_col_DataFrame'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/i386/CNEr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeGRBs        33.32   1.93   37.61
makeCNEDensity  21.81   0.24   22.19
plotCNEWidth    13.18   0.00   13.18
syntenicDotplot  5.54   0.04    7.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeGRBs        31.37   1.89   33.27
makeCNEDensity  23.31   0.23   24.31
plotCNEWidth    16.55   0.07   16.62
syntenicDotplot  5.08   0.08    6.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/CNEr.Rcheck/00check.log'
for details.

CNEr.Rcheck/00install.out:


install for i386

* installing *source* package 'CNEr' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'CNEr'
** 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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/CNEr.buildbin-libdir/CNEr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNEr' as CNEr_1.9.39.zip
* DONE (CNEr)

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

nameusersystemelapsed
AssemblyStats0.000.001.45
Axt-class0.750.030.78
Axt-util0.060.000.06
CNE-class0.190.020.20
CNEDanRer10Hg380.010.000.02
CNEDensity0.580.000.57
GRangePairs-class0.530.030.57
axisTrack0.000.010.02
axtChain000
axtInfo0.020.000.01
binner000
blatCNE000
ceScan-methods0.790.071.42
chainMergeSort000
chainNetSyntenic000
chainPreNet000
cneFinalListDanRer10Hg380.070.010.08
cneMerge0.610.000.61
fetchChromSizes000
fixCoordinates0.690.000.69
grangesPairsForDotplot0.000.020.01
last000
lastz000
lavToPsl000
makeAncoraFiles0.060.010.11
makeCNEDensity21.81 0.2422.19
makeGRBs33.32 1.9337.61
matchDistribution0.250.000.25
netToAxt000
plotCNEDistribution0.660.000.65
plotCNEWidth13.18 0.0013.18
psubAxt0.390.000.39
read.rmMask.GRanges0.050.000.13
readAncora0.090.000.09
readAncoraIntoSQLite2.120.022.14
readAxt0.070.000.06
readBed0.030.000.03
readCNERangesFromSQLite0.120.000.13
reverseCigar000
saveCNEToSQLite0.160.010.17
scoringMatrix000
subAxt-methods1.090.021.11
syntenicDotplot5.540.047.80
writeAxt0.030.000.03

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

nameusersystemelapsed
AssemblyStats0.010.000.02
Axt-class0.560.020.57
Axt-util0.030.000.03
CNE-class0.190.000.19
CNEDanRer10Hg380.010.000.01
CNEDensity0.720.000.72
GRangePairs-class0.420.000.45
axisTrack000
axtChain000
axtInfo000
binner000
blatCNE000
ceScan-methods0.550.091.42
chainMergeSort000
chainNetSyntenic000
chainPreNet000
cneFinalListDanRer10Hg380.030.000.03
cneMerge0.450.020.47
fetchChromSizes000
fixCoordinates0.930.020.95
grangesPairsForDotplot000
last000
lastz000
lavToPsl000
makeAncoraFiles0.060.000.08
makeCNEDensity23.31 0.2324.31
makeGRBs31.37 1.8933.27
matchDistribution0.300.010.31
netToAxt000
plotCNEDistribution0.810.000.81
plotCNEWidth16.55 0.0716.62
psubAxt0.460.000.46
read.rmMask.GRanges0.030.000.03
readAncora0.070.000.06
readAncoraIntoSQLite1.230.001.24
readAxt0.030.000.03
readBed0.020.010.03
readCNERangesFromSQLite0.060.020.08
reverseCigar0.010.000.01
saveCNEToSQLite0.170.000.17
scoringMatrix000
subAxt-methods1.140.011.15
syntenicDotplot5.080.086.95
writeAxt0.040.000.03