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BioC 3.4: CHECK report for kebabs on zin1

This page was generated on 2016-09-21 03:39:26 -0700 (Wed, 21 Sep 2016).

Package 641/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.7.3
Ulrich Bodenhofer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs
Last Changed Rev: 120614 / Revision: 121152
Last Changed Date: 2016-08-31 01:23:38 -0700 (Wed, 31 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.7.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings kebabs_1.7.3.tar.gz
StartedAt: 2016-09-20 08:29:27 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:32:53 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 206.6 seconds
RetCode: 0
Status:  OK 
CheckDir: kebabs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings kebabs_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/kebabs.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.3’
* 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  8.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.9Mb
* 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 8.576      0   8.574
* 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-3.4-bioc/meat/kebabs.Rcheck/00check.log’
for details.

kebabs.Rcheck/00install.out:

* installing *source* package ‘kebabs’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c svm.cpp -o svm.o
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
BioVector0.0240.0000.025
CrossValidationResultAccessors0.0040.0000.002
KBModelAccessors0.0000.0000.001
KernelMatrixAccessors0.0000.0000.001
LinearKernel4.2720.0284.298
ModelSelectionResultAccessors0.0000.0000.002
PredictionProfileAccessors0.0000.0000.002
ROCDataAccessors0.0040.0000.001
SVMAccess0.0880.0000.090
annotationSpecificKernel0.0840.0000.087
computeROCandAUC1.2880.0441.966
evaluatePrediction0.4280.0080.438
explicitRepresentation0.0520.0040.057
featureWeights0.2400.0040.244
gappyPairKernel0.0080.0000.007
genRandBioSeqs0.0480.0000.051
getPredProfMixture-methods3.1080.6443.753
getPredictionProfile-methods0.6040.3040.909
heatmap-methods0.3480.1760.525
kbsvm-methods0.1760.0040.176
kebabsCollectInfo0.0160.0360.055
kebabsOverview0.2480.0480.295
mismatchKernel0.0080.0000.008
motifKernel0.0080.0000.007
performCrossValidation-methods0.2160.0080.223
performGridSearch3.7560.0243.781
performModelSelection8.5760.0008.574
plot-methods0.6080.0120.631
positionDependentKernel0.0120.0000.012
predict-methods0.2520.0040.258
sequenceKernel0.0280.0000.029
show-methods0.0240.0000.022
spectrumKernel0.0080.0000.006
symmetricPairKernel0.1000.0120.111