Package: kebabs

Version: 1.14.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings kebabs_1.14.0.tar.gz

StartedAt: 2018-10-16 01:27:31 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:29:57 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 146.2 seconds

RetCode: 0

Status:  OK

CheckDir: kebabs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings kebabs_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/kebabs.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.2Mb
    libs   6.0Mb
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
performModelSelection 10.196  0.096  10.305
performGridSearch      5.172  0.092   5.270
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/kebabs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL kebabs
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function ‘SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)’:
MismatchC.cpp:432:41: warning: ‘currValSqrt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                     km(i,j) = kernelVal / currValSqrt;
                                         ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c MotifC.cpp -o MotifC.o
MotifC.cpp: In function ‘void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)’:
MotifC.cpp:3677:27: warning: ‘keyPool’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         pKeypool = keyPool;
                           ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c svm.cpp -o svm.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/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 -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/kebabs/libs
** R
** data
** inst
** byte-compile and prepare 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	0.036	0.000	0.037
CrossValidationResultAccessors	0.004	0.000	0.002
KBModelAccessors	0.004	0.000	0.002
KernelMatrixAccessors	0.000	0.000	0.001
LinearKernel	4.152	0.016	4.190
ModelSelectionResultAccessors	0.000	0.000	0.002
PredictionProfileAccessors	0.004	0.000	0.002
ROCDataAccessors	0.000	0.000	0.002
SVMAccess	0.092	0.004	0.094
annotationSpecificKernel	0.096	0.004	0.099
computeROCandAUC	1.368	0.096	1.471
evaluatePrediction	0.672	0.000	0.675
explicitRepresentation	0.148	0.004	0.152
featureWeights	0.592	0.020	0.613
gappyPairKernel	0.008	0.000	0.008
genRandBioSeqs	0.048	0.000	0.046
getPredProfMixture-methods	3.992	0.484	4.492
getPredictionProfile-methods	0.632	0.120	0.754
heatmap-methods	0.752	0.144	0.901
kbsvm-methods	0.196	0.000	0.195
kebabsCollectInfo	0.052	0.064	0.129
kebabsOverview	0.288	0.044	0.330
mismatchKernel	0.008	0.000	0.008
motifKernel	0.016	0.000	0.031
performCrossValidation-methods	0.364	0.048	0.415
performGridSearch	5.172	0.092	5.270
performModelSelection	10.196	0.096	10.305
plot-methods	0.428	0.004	0.433
positionDependentKernel	0.012	0.000	0.012
predict-methods	0.252	0.000	0.251
sequenceKernel	0.036	0.004	0.038
show-methods	0.020	0.000	0.021
spectrumKernel	0.004	0.000	0.006
symmetricPairKernel	0.132	0.000	0.130