Back to Multiple platform build/check report for BioC 3.9
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for chromVAR on malbec2

This page was generated on 2019-10-16 12:12:17 -0400 (Wed, 16 Oct 2019).

Package 275/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.6.0
Alicia Schep
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chromVAR
Branch: RELEASE_3_9
Last Commit: 6305c5e
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromVAR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromVAR_1.6.0.tar.gz
StartedAt: 2019-10-16 00:32:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:38:45 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 400.8 seconds
RetCode: 0
Status:  OK 
CheckDir: chromVAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromVAR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 ‘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 20.700  0.288  21.304
getJasparMotifs          7.168  0.052   7.221
pwmDistance              6.576  0.075   6.661
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck/00check.log’
for details.



Installation output

chromVAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL chromVAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pwm_similarity.cpp -o pwm_similarity.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’:
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                   ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-chromVAR/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chromVAR)

Tests output

chromVAR.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.787   1.246  25.245 

Example timings

chromVAR.Rcheck/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias1.0160.0241.040
annotationMatches0.0170.0040.022
chromVAR_theme0.8950.0000.897
computeDeviations3.9640.5234.485
computeExpectations0.0310.0000.031
computeVariability4.1410.1524.293
counts0.0080.0000.008
deviationScores0.0060.0000.006
deviations0.0060.0000.006
deviationsCovariability20.700 0.28821.304
deviationsTsne0.0900.0040.094
differentialDeviations0.0170.0000.017
differentialVariability0.0360.0000.036
example_counts0.0010.0000.001
filterPeaks0.2580.0000.259
filterSamples0.0750.0000.075
filterSamplesPlot0.1610.0000.161
getAnnotations0.4790.0040.484
getBackgroundPeaks0.9910.0721.064
getCisGroups0.0770.0000.077
getCounts4.4990.1244.657
getFragmentsPerPeak0.0120.0000.012
getFragmentsPerSample0.0120.0000.012
getJasparMotifs7.1680.0527.221
getPeaks0.0620.0000.063
getPermutedData1.2620.1401.402
getSampleCorrelation0.0110.0000.011
getSampleDepths0.0800.0160.095
getSampleDistance0.0120.0000.011
getTotalFragments0.0090.0000.008
makeBiasBins0.0310.0040.034
makePermutedSets1.0280.0121.047
matchKmers1.3130.0321.345
mini_counts0.0010.0000.001
mini_dev0.0000.0000.001
mini_ix0.0010.0000.001
plotVariability3.6210.0403.672
pwmDistance6.5760.0756.661
rbind-chromVARDeviations-method0.0640.0000.064