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BioC 3.0: CHECK report for CNEr on perceval

This page was generated on 2015-04-10 09:59:16 -0700 (Fri, 10 Apr 2015).

Package 174/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.2.0
Ge Tan
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CNEr
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: CNEr
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNEr_1.2.0.tar.gz
StartedAt: 2015-04-10 00:05:14 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:12:01 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 406.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CNEr.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNEr_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CNEr.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNEr’ can be installed ... [35s/70s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readBedR: no visible global function definition for ‘strand<-’
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘CNEr/libs/CNEr.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’,
      ‘ucsc/verbose.o’, ‘ucsc/os.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’,
      ‘ucsc/os.o’
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘ucsc/errabort.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘ceScan.o’, ‘ucsc/pipeline.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘ucsc/pipeline.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ucsc/obscure.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/27s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
cneMerge 6.991  0.054   7.147
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/16s]
 [14s/18s] 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

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CNEr.Rcheck/00check.log’
for details.

CNEr.Rcheck/00install.out:

* installing *source* package ‘CNEr’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_CNEr.c -o R_init_CNEr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c utils.c -o utils.o
utils.c: In function ‘bin_ranges_from_coord_range_standard’:
utils.c:50: warning: unused variable ‘_binNextShift’
utils.c:49: warning: unused variable ‘_binFirstShift’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c io.c -o io.o
io.c: In function ‘myReadAxt’:
io.c:94: warning: unused variable ‘curAxt’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ceScan.c -o ceScan.o
ceScan.c: In function ‘ceScan’:
ceScan.c:615: warning: unused variable ‘rest’
ceScan.c:613: warning: unused variable ‘n’
ceScan.c: In function ‘freeSlThreshold’:
ceScan.c:674: warning: unused variable ‘CNE’
ceScan.c:673: warning: unused variable ‘thresholds’
ceScan.c: In function ‘myCeScan’:
ceScan.c:865: warning: unused variable ‘i’
ceScan.c:865: warning: unused variable ‘nrCNE’
ceScan.c:862: warning: unused variable ‘CNE’
ceScan.c: In function ‘myCeScanFile’:
ceScan.c:895: warning: unused variable ‘nrThresholds’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/axt.c -o ucsc/axt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/base64.c -o ucsc/base64.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/binRange.c -o ucsc/binRange.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/bits.c -o ucsc/bits.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/chain.c -o ucsc/chain.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/cirTree.c -o ucsc/cirTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/common.c -o ucsc/common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/dlist.c -o ucsc/dlist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/dnautil.c -o ucsc/dnautil.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/dystring.c -o ucsc/dystring.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/errabort.c -o ucsc/errabort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/hash.c -o ucsc/hash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/https.c -o ucsc/https.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/intExp.c -o ucsc/intExp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/kxTok.c -o ucsc/kxTok.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/linefile.c -o ucsc/linefile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/localmem.c -o ucsc/localmem.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/memalloc.c -o ucsc/memalloc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/obscure.c -o ucsc/obscure.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/options.c -o ucsc/options.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/pipeline.c -o ucsc/pipeline.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/sqlList.c -o ucsc/sqlList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/verbose.c -o ucsc/verbose.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/os.c -o ucsc/os.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"  -g -fPIC  -mtune=core2 -g -O2 -Wall  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CNEr.so 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 -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/CNEr.Rcheck/CNEr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNEr)

CNEr.Rcheck/CNEr-Ex.timings:

nameusersystemelapsed
CNE-class0.0020.0000.002
CNEDensity1.4970.0192.482
CNEHg19DanRer70.0220.0040.087
axisTrack0.0060.0010.073
axt-class0.0010.0000.002
axtDanRer7Hg190.0080.0020.010
axtInfo000
binner0.0030.0010.002
blatCNE0.0010.0000.001
ceScan-methods0.0010.0000.001
cneBlatedDanRer7Hg190.0220.0040.117
cneHg19DanRer7_45_500.0050.0010.078
cneMerge6.9910.0547.147
fetchChromSizes0.0260.0050.643
finalCNE0.0030.0010.003
qSizesDanRer70.0050.0010.023
readAxt0.0000.0000.001
readBed0.0170.0020.018
readCNERangesFromSQLite0.0100.0020.012
reverseCigar0.0010.0000.002
saveCNEToSQLite0.1130.0140.371
subAxt-methods0.0000.0000.001
writeAxt0.0010.0000.001