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CHECK report for chromVAR on merida1

This page was generated on 2019-04-16 12:01:40 -0400 (Tue, 16 Apr 2019).

Package 261/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.4.1
Alicia Schep
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/chromVAR
Branch: RELEASE_3_8
Last Commit: e185549
Last Changed Date: 2019-01-04 13:14:02 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chromVAR
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.4.1.tar.gz
StartedAt: 2019-04-15 22:59:57 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:06:50 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 412.5 seconds
RetCode: 0
Status:  OK 
CheckDir: chromVAR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/chromVAR.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 ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.4.1’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
deviationsCovariability 25.746  0.481  26.624
getJasparMotifs          8.074  0.142   8.299
pwmDistance              7.410  0.126   7.622
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/chromVAR.Rcheck/00check.log’
for details.



Installation output

chromVAR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromVAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘chromVAR’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/chromVAR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (chromVAR)

Tests output

chromVAR.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
 25.124   1.270  26.673 

Example timings

chromVAR.Rcheck/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias0.8860.0290.925
annotationMatches0.0210.0020.023
chromVAR_theme0.0360.0030.038
computeDeviations3.0890.1223.250
computeExpectations0.0350.0010.035
computeVariability4.4600.1184.618
counts0.0150.0010.016
deviationScores0.0080.0010.008
deviations0.0070.0000.007
deviationsCovariability25.746 0.48126.624
deviationsTsne0.1160.0020.121
differentialDeviations0.0180.0010.019
differentialVariability0.0400.0010.040
example_counts0.0010.0010.003
filterPeaks0.3000.0140.317
filterSamples0.0830.0090.094
filterSamplesPlot0.1590.0090.174
getAnnotations0.5020.0090.516
getBackgroundPeaks0.9960.0931.109
getCisGroups0.1030.0000.105
getCounts4.1010.2884.455
getFragmentsPerPeak0.0150.0010.016
getFragmentsPerSample0.0160.0010.017
getJasparMotifs8.0740.1428.299
getPeaks0.1170.0020.120
getPermutedData2.7210.1322.890
getSampleCorrelation0.0210.0010.022
getSampleDepths0.1560.0060.168
getSampleDistance0.0210.0000.022
getTotalFragments0.0160.0000.016
makeBiasBins0.0590.0010.059
makePermutedSets1.2940.0691.377
matchKmers1.5510.0681.646
mini_counts0.0010.0010.003
mini_dev0.0020.0010.003
mini_ix0.0020.0010.003
plotVariability4.8440.0644.960
pwmDistance7.4100.1267.622
rbind-chromVARDeviations-method0.0460.0010.046