Alicia Schep
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: RELEASE_3_6 |
| Last Commit: bb0722d |
| Last Changed Date: 2018-04-02 13:48:25 -0400 (Mon, 02 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:45:52 -0400 (Thu, 12 Apr 2018).
| Package 233/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.0.2 Alicia Schep
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: chromVAR |
| Version: 1.0.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromVAR_1.0.2.tar.gz |
| StartedAt: 2018-04-12 01:43:24 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:49:56 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 391.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromVAR_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chromVAR.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 ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.0.2’
* 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 ‘chromVAR’ 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 loading without being on the library search path ... 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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
deviationsCovariability 17.716 0.373 18.602
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
chromVAR.Rcheck/00install.out
* installing *source* package ‘chromVAR’ ... ** libs clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -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 chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/chromVAR.Rcheck/chromVAR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (chromVAR)
chromVAR.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(chromVAR)
> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 65 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
19.869 0.604 20.895
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.794 | 0.047 | 1.911 | |
| annotationMatches | 0.013 | 0.002 | 0.015 | |
| chromVAR_theme | 0.130 | 0.016 | 0.147 | |
| computeDeviations | 2.542 | 0.106 | 2.751 | |
| computeExpectations | 0.01 | 0.00 | 0.01 | |
| computeVariability | 0.974 | 0.021 | 1.009 | |
| counts | 0.008 | 0.001 | 0.007 | |
| deviationScores | 0.005 | 0.000 | 0.005 | |
| deviations | 0.006 | 0.000 | 0.006 | |
| deviationsCovariability | 17.716 | 0.373 | 18.602 | |
| deviationsTsne | 0.222 | 0.002 | 0.265 | |
| differentialDeviations | 0.011 | 0.000 | 0.013 | |
| differentialVariability | 0.029 | 0.001 | 0.029 | |
| example_counts | 0.002 | 0.001 | 0.002 | |
| filterPeaks | 0.380 | 0.012 | 0.413 | |
| filterSamples | 0.085 | 0.007 | 0.092 | |
| filterSamplesPlot | 0.194 | 0.021 | 0.227 | |
| getAnnotations | 0.497 | 0.006 | 0.523 | |
| getBackgroundPeaks | 1.176 | 0.079 | 1.282 | |
| getCisGroups | 0.079 | 0.001 | 0.079 | |
| getCounts | 3.438 | 0.148 | 3.641 | |
| getFragmentsPerPeak | 0.007 | 0.001 | 0.009 | |
| getFragmentsPerSample | 0.008 | 0.000 | 0.008 | |
| getJasparMotifs | 2.568 | 0.096 | 2.718 | |
| getPeaks | 0.224 | 0.001 | 0.231 | |
| getPermutedData | 1.535 | 0.133 | 1.694 | |
| getSampleCorrelation | 0.023 | 0.000 | 0.024 | |
| getSampleDepths | 0.226 | 0.018 | 0.246 | |
| getSampleDistance | 0.006 | 0.001 | 0.006 | |
| getTotalFragments | 0.007 | 0.000 | 0.007 | |
| makeBiasBins | 0.027 | 0.001 | 0.026 | |
| makePermutedSets | 0.995 | 0.048 | 1.082 | |
| matchKmers | 1.919 | 0.050 | 2.013 | |
| mini_counts | 0.002 | 0.001 | 0.003 | |
| mini_dev | 0.002 | 0.001 | 0.002 | |
| mini_ix | 0.002 | 0.001 | 0.002 | |
| plotVariability | 0.448 | 0.005 | 0.475 | |
| pwmDistance | 3.180 | 0.124 | 3.370 | |
| rbind-chromVARDeviations-method | 0.073 | 0.001 | 0.075 | |