Ulrich Bodenhofer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/kebabs |
| Branch: RELEASE_3_8 |
| Last Commit: 726b350 |
| Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:07 -0400 (Tue, 16 Apr 2019).
| Package 815/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| kebabs 1.16.0 Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: kebabs |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kebabs_1.16.0.tar.gz |
| StartedAt: 2019-04-16 00:50:06 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:53:27 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 200.4 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 --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kebabs_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/kebabs.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
performModelSelection 11.026 2.653 13.763
performGridSearch 5.801 1.129 6.971
getPredProfMixture-methods 4.399 0.752 5.200
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL kebabs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘kebabs’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/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)
kebabs.Rcheck/kebabs-Ex.timings
| name | user | system | elapsed | |
| BioVector | 0.040 | 0.002 | 0.041 | |
| CrossValidationResultAccessors | 0.002 | 0.000 | 0.002 | |
| KBModelAccessors | 0.001 | 0.000 | 0.001 | |
| KernelMatrixAccessors | 0.001 | 0.000 | 0.001 | |
| LinearKernel | 3.723 | 0.049 | 3.808 | |
| ModelSelectionResultAccessors | 0.001 | 0.001 | 0.001 | |
| PredictionProfileAccessors | 0.001 | 0.000 | 0.002 | |
| ROCDataAccessors | 0.001 | 0.000 | 0.001 | |
| SVMAccess | 0.087 | 0.009 | 0.095 | |
| annotationSpecificKernel | 0.101 | 0.004 | 0.106 | |
| computeROCandAUC | 1.714 | 0.298 | 2.017 | |
| evaluatePrediction | 0.701 | 0.095 | 0.796 | |
| explicitRepresentation | 0.161 | 0.003 | 0.163 | |
| featureWeights | 0.679 | 0.048 | 0.731 | |
| gappyPairKernel | 0.009 | 0.001 | 0.010 | |
| genRandBioSeqs | 0.052 | 0.001 | 0.054 | |
| getPredProfMixture-methods | 4.399 | 0.752 | 5.200 | |
| getPredictionProfile-methods | 0.770 | 0.115 | 0.888 | |
| heatmap-methods | 0.910 | 0.261 | 1.178 | |
| kbsvm-methods | 0.234 | 0.017 | 0.252 | |
| kebabsCollectInfo | 0.055 | 0.011 | 0.068 | |
| kebabsOverview | 0.368 | 0.040 | 0.410 | |
| mismatchKernel | 0.009 | 0.001 | 0.010 | |
| motifKernel | 0.011 | 0.001 | 0.012 | |
| performCrossValidation-methods | 0.282 | 0.109 | 0.398 | |
| performGridSearch | 5.801 | 1.129 | 6.971 | |
| performModelSelection | 11.026 | 2.653 | 13.763 | |
| plot-methods | 0.530 | 0.111 | 0.644 | |
| positionDependentKernel | 0.016 | 0.001 | 0.018 | |
| predict-methods | 0.364 | 0.025 | 0.392 | |
| sequenceKernel | 0.055 | 0.003 | 0.061 | |
| show-methods | 0.024 | 0.006 | 0.031 | |
| spectrumKernel | 0.009 | 0.001 | 0.010 | |
| symmetricPairKernel | 0.190 | 0.035 | 0.253 | |