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CHECK report for chromVAR on veracruz1

This page was generated on 2018-04-12 13:45:52 -0400 (Thu, 12 Apr 2018).

Package 233/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.0.2
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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromVAR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* 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


Installation output

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)

Tests output

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 

Example timings

chromVAR.Rcheck/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias1.7940.0471.911
annotationMatches0.0130.0020.015
chromVAR_theme0.1300.0160.147
computeDeviations2.5420.1062.751
computeExpectations0.010.000.01
computeVariability0.9740.0211.009
counts0.0080.0010.007
deviationScores0.0050.0000.005
deviations0.0060.0000.006
deviationsCovariability17.716 0.37318.602
deviationsTsne0.2220.0020.265
differentialDeviations0.0110.0000.013
differentialVariability0.0290.0010.029
example_counts0.0020.0010.002
filterPeaks0.3800.0120.413
filterSamples0.0850.0070.092
filterSamplesPlot0.1940.0210.227
getAnnotations0.4970.0060.523
getBackgroundPeaks1.1760.0791.282
getCisGroups0.0790.0010.079
getCounts3.4380.1483.641
getFragmentsPerPeak0.0070.0010.009
getFragmentsPerSample0.0080.0000.008
getJasparMotifs2.5680.0962.718
getPeaks0.2240.0010.231
getPermutedData1.5350.1331.694
getSampleCorrelation0.0230.0000.024
getSampleDepths0.2260.0180.246
getSampleDistance0.0060.0010.006
getTotalFragments0.0070.0000.007
makeBiasBins0.0270.0010.026
makePermutedSets0.9950.0481.082
matchKmers1.9190.0502.013
mini_counts0.0020.0010.003
mini_dev0.0020.0010.002
mini_ix0.0020.0010.002
plotVariability0.4480.0050.475
pwmDistance3.1800.1243.370
rbind-chromVARDeviations-method0.0730.0010.075