Ulrich Bodenhofer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/kebabs |
| Branch: RELEASE_3_6 |
| Last Commit: 365df61 |
| Last Changed Date: 2017-10-30 12:40:44 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:45 -0400 (Thu, 12 Apr 2018).
| Package 731/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| kebabs 1.12.0 Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: kebabs |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kebabs_1.12.0.tar.gz |
| StartedAt: 2018-04-12 05:31:44 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:36:19 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 274.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings kebabs_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/kebabs.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 ... 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 8.400 1.788 10.335
LinearKernel 4.223 0.054 5.412
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
* installing *source* package ‘kebabs’ ... ** libs clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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 /Users/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
| name | user | system | elapsed | |
| BioVector | 0.117 | 0.008 | 0.127 | |
| CrossValidationResultAccessors | 0.003 | 0.000 | 0.003 | |
| KBModelAccessors | 0.058 | 0.008 | 0.068 | |
| KernelMatrixAccessors | 0.002 | 0.000 | 0.002 | |
| LinearKernel | 4.223 | 0.054 | 5.412 | |
| ModelSelectionResultAccessors | 0.002 | 0.000 | 0.008 | |
| PredictionProfileAccessors | 0.003 | 0.000 | 0.003 | |
| ROCDataAccessors | 0.002 | 0.001 | 0.002 | |
| SVMAccess | 0.098 | 0.009 | 0.107 | |
| annotationSpecificKernel | 0.740 | 0.030 | 0.784 | |
| computeROCandAUC | 1.944 | 0.165 | 2.145 | |
| evaluatePrediction | 1.331 | 0.053 | 1.406 | |
| explicitRepresentation | 0.214 | 0.005 | 0.224 | |
| featureWeights | 0.458 | 0.030 | 0.502 | |
| gappyPairKernel | 0.007 | 0.001 | 0.008 | |
| genRandBioSeqs | 0.054 | 0.001 | 0.056 | |
| getPredProfMixture-methods | 3.810 | 0.588 | 4.461 | |
| getPredictionProfile-methods | 1.307 | 0.207 | 1.553 | |
| heatmap-methods | 0.465 | 0.136 | 0.603 | |
| kbsvm-methods | 0.208 | 0.032 | 0.240 | |
| kebabsCollectInfo | 0.036 | 0.008 | 0.045 | |
| kebabsOverview | 0.256 | 0.043 | 0.303 | |
| mismatchKernel | 0.079 | 0.001 | 0.081 | |
| motifKernel | 0.183 | 0.029 | 0.218 | |
| performCrossValidation-methods | 0.281 | 0.018 | 0.300 | |
| performGridSearch | 3.754 | 0.948 | 4.770 | |
| performModelSelection | 8.400 | 1.788 | 10.335 | |
| plot-methods | 0.437 | 0.082 | 0.526 | |
| positionDependentKernel | 0.011 | 0.001 | 0.012 | |
| predict-methods | 0.246 | 0.032 | 0.280 | |
| sequenceKernel | 0.045 | 0.006 | 0.052 | |
| show-methods | 0.023 | 0.003 | 0.026 | |
| spectrumKernel | 0.006 | 0.000 | 0.007 | |
| symmetricPairKernel | 0.123 | 0.017 | 0.142 | |