Package: kebabs

Version: 1.17.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings kebabs_1.17.0.tar.gz

StartedAt: 2019-04-09 01:31:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:34:34 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 192.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: kebabs.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings kebabs_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/kebabs.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.17.0’
* 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 ... WARNING
Found the following significant warnings:
  MismatchC.cpp:2308:47: warning: ‘alphaInf.alphaInfo::numAlphabetChars’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/kebabs.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.2Mb
    libs   6.2Mb
* 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 11.390  0.108  11.498
performGridSearch      6.933  0.092   7.027
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/kebabs.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function ‘void genPredProfileMismatch(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, bool, bool, bool)’:
MismatchC.cpp:2308:47: warning: ‘alphaInf.alphaInfo::numAlphabetChars’ is used uninitialized in this function [-Wuninitialized]
     dimFeatureSpace = pow((uint64_t) alphaInf.numAlphabetChars, k);
                                      ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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:3677:18: warning: ‘keyPool’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         pKeypool = keyPool;
         ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c svm.cpp -o svm.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-kebabs/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (kebabs)

name	user	system	elapsed
BioVector	0.034	0.004	0.038
CrossValidationResultAccessors	0.001	0.000	0.001
KBModelAccessors	0.000	0.000	0.001
KernelMatrixAccessors	0.000	0.000	0.001
LinearKernel	4.362	0.036	4.419
ModelSelectionResultAccessors	0.001	0.000	0.000
PredictionProfileAccessors	0.001	0.000	0.001
ROCDataAccessors	0	0	0
SVMAccess	0.085	0.000	0.085
annotationSpecificKernel	0.097	0.000	0.098
computeROCandAUC	1.880	0.064	1.946
evaluatePrediction	0.599	0.004	0.603
explicitRepresentation	0.14	0.00	0.14
featureWeights	0.244	0.008	0.252
gappyPairKernel	0.005	0.000	0.005
genRandBioSeqs	0.046	0.000	0.047
getPredProfMixture-methods	2.486	0.144	2.630
getPredictionProfile-methods	0.580	0.028	0.608
heatmap-methods	0.337	0.040	0.377
kbsvm-methods	0.199	0.008	0.207
kebabsCollectInfo	0.034	0.000	0.034
kebabsOverview	0.299	0.028	0.328
mismatchKernel	0.009	0.000	0.009
motifKernel	0.008	0.000	0.018
performCrossValidation-methods	0.379	0.008	0.387
performGridSearch	6.933	0.092	7.027
performModelSelection	11.390	0.108	11.498
plot-methods	0.433	0.000	0.433
positionDependentKernel	0.009	0.000	0.008
predict-methods	0.305	0.004	0.308
sequenceKernel	0.033	0.004	0.038
show-methods	0.02	0.00	0.02
spectrumKernel	0.004	0.000	0.005
symmetricPairKernel	0.098	0.012	0.111