BioC 3.5: CHECK report for kebabs on veracruz2

Package: kebabs

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kebabs_1.10.0.tar.gz

StartedAt: 2017-08-16 04:31:40 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:36:15 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 275.0 seconds

RetCode: 0

Status:  OK

CheckDir: kebabs.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kebabs_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/kebabs.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 ‘kebabs’ can be installed ... 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
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’
Undefined global functions or variables:
  ccseq enhancerFB yCC yFB
* 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
performModelSelection 8.846  1.961  11.093
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/kebabs.Rcheck/00check.log’
for details.

* installing *source* package ‘kebabs’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ByteStringVector.c -o ByteStringVector.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ExplicitRepC.cpp -o ExplicitRepC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c GappyPairC.cpp -o GappyPairC.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c KernelUtils.cpp -o KernelUtils.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MismatchC.cpp -o MismatchC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MotifC.cpp -o MotifC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PredictionC.cpp -o PredictionC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PredictionProfileC.cpp -o PredictionProfileC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_kebabs.cpp -o R_init_kebabs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rsvm.c -o Rsvm.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SpectrumC.cpp -o SpectrumC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SymmetricPairC.cpp -o SymmetricPairC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Utils.cpp -o Utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c svm.cpp -o svm.o
clang++ -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 -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 Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)

name	user	system	elapsed
BioVector	0.086	0.001	0.095
CrossValidationResultAccessors	0.003	0.000	0.003
KBModelAccessors	0.048	0.001	0.050
KernelMatrixAccessors	0.001	0.000	0.001
LinearKernel	4.026	0.038	4.177
ModelSelectionResultAccessors	0.002	0.000	0.002
PredictionProfileAccessors	0.002	0.000	0.003
ROCDataAccessors	0.002	0.001	0.002
SVMAccess	0.083	0.007	0.090
annotationSpecificKernel	0.480	0.023	0.518
computeROCandAUC	1.961	0.150	2.170
evaluatePrediction	1.190	0.071	1.282
explicitRepresentation	0.167	0.002	0.169
featureWeights	0.223	0.021	0.248
gappyPairKernel	0.008	0.000	0.008
genRandBioSeqs	0.046	0.000	0.046
getPredProfMixture-methods	4.152	0.507	4.809
getPredictionProfile-methods	1.422	0.199	1.667
heatmap-methods	0.433	0.144	0.596
kbsvm-methods	0.231	0.015	0.246
kebabsCollectInfo	0.030	0.006	0.038
kebabsOverview	0.273	0.032	0.321
mismatchKernel	0.102	0.001	0.109
motifKernel	0.177	0.002	0.182
performCrossValidation-methods	0.292	0.051	0.354
performGridSearch	3.937	0.879	4.957
performModelSelection	8.846	1.961	11.093
plot-methods	0.370	0.074	0.470
positionDependentKernel	0.009	0.001	0.010
predict-methods	0.254	0.032	0.315
sequenceKernel	0.045	0.001	0.046
show-methods	0.022	0.004	0.027
spectrumKernel	0.006	0.000	0.007
symmetricPairKernel	0.118	0.019	0.138