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This page was generated on 2021-09-20 15:04:45 -0400 (Mon, 20 Sep 2021).

CHECK results for chromVAR on nebbiolo1

To the developers/maintainers of the chromVAR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromVAR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 309/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.14.0  (landing page)
Alicia Schep
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/chromVAR
git_branch: RELEASE_3_13
git_last_commit: 2dc5547
git_last_commit_date: 2021-05-19 12:30:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chromVAR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromVAR_1.14.0.tar.gz
StartedAt: 2021-09-19 09:13:10 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:19:57 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 406.9 seconds
RetCode: 0
Status:   OK  
CheckDir: chromVAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromVAR_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/chromVAR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.14.0’
* 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 LazyData ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plotVariability         27.463  0.221  27.689
deviationsCovariability 24.197  1.952  26.166
computeVariability      23.997  0.284  24.282
getJasparMotifs          5.457  0.123   5.581
pwmDistance              5.209  0.148   5.357
getCounts                5.044  0.183   5.240
* 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-3.13-bioc/meat/chromVAR.Rcheck/00check.log’
for details.



Installation output

chromVAR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL chromVAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   12 |     for( int j=0; j < X.n_rows; j++ ) {
      |                   ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 22.227   1.036  23.241 

Example timings

chromVAR.Rcheck/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias0.6710.0600.731
annotationMatches0.0160.0040.020
chromVAR_theme0.0140.0040.018
computeDeviations4.1670.1674.331
computeExpectations0.0330.0000.033
computeVariability23.997 0.28424.282
counts0.0200.0100.031
deviationScores0.020.000.02
deviations0.0150.0040.020
deviationsCovariability24.197 1.95226.166
deviationsTsne0.0630.0000.063
differentialDeviations0.0150.0000.015
differentialVariability0.0270.0000.027
example_counts0.0010.0000.001
filterPeaks0.2690.0080.278
filterSamples0.0720.0070.079
filterSamplesPlot0.1220.0120.134
getAnnotations0.4610.0000.462
getBackgroundPeaks0.5060.1080.614
getCisGroups0.4350.0080.443
getCounts5.0440.1835.240
getFragmentsPerPeak0.0130.0000.014
getFragmentsPerSample0.0090.0040.013
getJasparMotifs5.4570.1235.581
getPeaks0.1900.0000.188
getPermutedData1.1110.1841.295
getSampleCorrelation0.0180.0040.022
getSampleDepths0.0810.0200.101
getSampleDistance0.020.000.02
getTotalFragments0.0130.0000.014
makeBiasBins0.0650.0040.069
makePermutedSets1.1900.1081.298
matchKmers1.1760.1441.320
mini_counts0.0010.0000.002
mini_dev0.0000.0010.001
mini_ix0.0000.0010.001
plotVariability27.463 0.22127.689
pwmDistance5.2090.1485.357
rbind-chromVARDeviations-method0.0880.0000.088