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BioC 3.0: CHECK report for kebabs on perceval

This page was generated on 2015-04-10 10:00:40 -0700 (Fri, 10 Apr 2015).

Package 475/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.0.5
Ulrich Bodenhofer
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/kebabs
Last Changed Rev: 100131 / Revision: 102249
Last Changed Date: 2015-03-03 13:23:27 -0800 (Tue, 03 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: kebabs
Version: 1.0.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch kebabs_1.0.5.tar.gz
StartedAt: 2015-04-10 03:04:05 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:11:46 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 461.0 seconds
RetCode: 0
Status:  OK 
CheckDir: kebabs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch kebabs_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/kebabs.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 ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.0.5’
* 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 ‘kebabs’ can be installed ... [93s/99s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘SparseM’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kebabsDemo: no visible binding for global variable ‘enhancerFB’
kebabsDemo: no visible binding for global variable ‘yFB’
kebabsDemo: no visible binding for global variable ‘ccseq’
kebabsDemo: no visible binding for global variable ‘yCC’
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/66s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
performModelSelection 18.536  0.058  18.604
performGridSearch      8.193  0.094   8.291
LinearKernel           6.377  0.077   6.456
evaluatePrediction     1.838  0.332   9.374
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/kebabs.Rcheck/00check.log’
for details.

kebabs.Rcheck/00install.out:

* installing *source* package ‘kebabs’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ByteStringVector.c -o ByteStringVector.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ExplicitRepC.cpp -o ExplicitRepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned char]’:
GappyPairC.cpp:3474:   instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’:
GappyPairC.cpp:3480:   instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = short unsigned int]’:
GappyPairC.cpp:3492:   instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = short unsigned int]’:
GappyPairC.cpp:3498:   instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned int]’:
GappyPairC.cpp:3511:   instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned int]’:
GappyPairC.cpp:3517:   instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = long long unsigned int]’:
GappyPairC.cpp:3529:   instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = long long unsigned int]’:
GappyPairC.cpp:3535:   instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c KernelUtils.cpp -o KernelUtils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MismatchC.cpp -o MismatchC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MotifC.cpp -o MotifC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PredictionC.cpp -o PredictionC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PredictionProfileC.cpp -o PredictionProfileC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_kebabs.cpp -o R_init_kebabs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned char]’:
SpectrumC.cpp:3222:   instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’:
SpectrumC.cpp:3228:   instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = short unsigned int]’:
SpectrumC.cpp:3240:   instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = short unsigned int]’:
SpectrumC.cpp:3246:   instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned int]’:
SpectrumC.cpp:3259:   instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned int]’:
SpectrumC.cpp:3265:   instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = long long unsigned int]’:
SpectrumC.cpp:3277:   instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = long long unsigned int]’:
SpectrumC.cpp:3283:   instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SymmetricPairC.cpp -o SymmetricPairC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Utils.cpp -o Utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/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" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-g++-4.2 -arch x86_64 -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 kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/kebabs.Rcheck/kebabs/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 (kebabs)

kebabs.Rcheck/kebabs-Ex.timings:

nameusersystemelapsed
BioVector0.0370.0010.038
KBModelAccessors0.0040.0000.003
KernelMatrixAccessors0.0020.0000.003
LinearKernel6.3770.0776.456
ModelSelectionResultAccessors0.0030.0000.003
PredictionProfileAccessors0.0030.0000.004
SVMAccess0.5650.0130.579
annotationSpecificKernel0.1460.0030.149
evaluatePrediction1.8380.3329.374
explicitRepresentation0.1180.0040.127
featureWeights1.6280.0301.742
gappyPairKernel0.0180.0020.019
genRandBioSeqs0.0850.0020.091
getPredictionProfile-methods1.8020.1582.008
kbsvm-methods0.8770.0850.963
kebabsOverview0.4850.0780.566
mismatchKernel0.0110.0000.013
motifKernel0.0120.0010.013
performCrossValidation-methods0.4220.0310.454
performGridSearch8.1930.0948.291
performModelSelection18.536 0.05818.604
plot-methods1.2760.0381.313
positionDependentKernel0.0170.0020.034
predict-methods0.4540.0340.488
sequenceKernel0.0440.0010.045
show-methods0.0330.0040.037
spectrumKernel0.0090.0010.010
symmetricPairKernel0.1690.0370.206