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BioC 3.6: CHECK report for kebabs on malbec1

This page was generated on 2017-08-16 13:22:36 -0400 (Wed, 16 Aug 2017).

Package 710/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.11.0
Ulrich Bodenhofer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.11.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings kebabs_1.11.0.tar.gz
StartedAt: 2017-08-16 00:14:53 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:18:56 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 242.5 seconds
RetCode: 0
Status:  OK 
CheckDir: kebabs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings kebabs_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/kebabs.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.11.0’
* 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  9.1Mb
  sub-directories of 1Mb or more:
    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 ... 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      9.616  0.012   9.633
getPredProfMixture-methods 3.948  2.296   6.257
LinearKernel               5.028  0.016   5.047
computeROCandAUC           2.324  0.144  16.659
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/kebabs.Rcheck/00check.log’
for details.

kebabs.Rcheck/00install.out:

* installing *source* package ‘kebabs’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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
BioVector0.0800.0000.079
CrossValidationResultAccessors0.0000.0000.002
KBModelAccessors0.0400.0000.039
KernelMatrixAccessors0.0040.0000.001
LinearKernel5.0280.0165.047
ModelSelectionResultAccessors0.0040.0000.002
PredictionProfileAccessors0.0040.0000.003
ROCDataAccessors0.0000.0000.001
SVMAccess0.1040.0000.102
annotationSpecificKernel0.4080.0160.424
computeROCandAUC 2.324 0.14416.659
evaluatePrediction1.1680.0161.183
explicitRepresentation0.1600.0000.159
featureWeights0.2240.0040.226
gappyPairKernel0.0160.0000.016
genRandBioSeqs0.0440.0000.043
getPredProfMixture-methods3.9482.2966.257
getPredictionProfile-methods1.1880.4761.667
heatmap-methods0.3360.4080.747
kbsvm-methods0.1800.0000.181
kebabsCollectInfo0.0320.0480.092
kebabsOverview0.2200.0440.264
mismatchKernel0.0760.0080.085
motifKernel0.1440.0080.151
performCrossValidation-methods0.2800.0040.281
performGridSearch4.1000.0404.144
performModelSelection9.6160.0129.633
plot-methods0.4120.0080.417
positionDependentKernel0.0120.0000.010
predict-methods0.2320.0080.241
sequenceKernel0.0320.0000.035
show-methods0.0200.0000.018
spectrumKernel0.0040.0000.005
symmetricPairKernel0.1200.0120.133