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CHECK report for ChIPSeqSpike on malbec2

This page was generated on 2020-10-17 11:54:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPSeqSpike PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 287/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPSeqSpike 1.8.0
Nicolas Descostes
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ChIPSeqSpike
Branch: RELEASE_3_11
Last Commit: be9b9b0
Last Changed Date: 2020-04-27 15:13:39 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPSeqSpike
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.8.0.tar.gz
StartedAt: 2020-10-16 23:48:45 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:55:31 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 406.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPSeqSpike.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ChIPSeqSpike.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPSeqSpike/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPSeqSpike’ version ‘1.8.0’
* 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 ‘ChIPSeqSpike’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
spikePipe              11.465  0.072  11.538
averageBindingValues   11.332  0.188  13.613
extractBinding         10.452  0.076  10.529
experimentList          8.237  0.048   8.286
count                   8.162  0.056   8.217
bigWigFile              8.034  0.060   8.093
exogenousScalingFactor  7.871  0.036   7.907
matBindingValues        7.796  0.056   7.851
scalingFactor           7.306  0.054   7.361
exoCount                7.258  0.044   7.301
* 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

ChIPSeqSpike.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ChIPSeqSpike
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ChIPSeqSpike’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ChIPSeqSpike.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPSeqSpike)

Tests output

ChIPSeqSpike.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("ChIPSeqSpike")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> proc.time()
   user  system elapsed 
 13.295   0.327  13.608 

Example timings

ChIPSeqSpike.Rcheck/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class0.0110.0000.011
ChIPSeqSpikeDatasetBoost-class0.6600.0000.718
ChIPSeqSpikeDatasetList-class0.0450.0000.145
ChIPSeqSpikeDatasetListBoost-class0.9580.0030.963
Experiment-class0.0020.0000.002
ExperimentLoaded-class0.1280.0000.128
averageBindingValues11.332 0.18813.613
bigWigFile8.0340.0608.093
boxplotSpike1.2660.0121.278
count8.1620.0568.217
datasetList0.2780.0000.279
estimateScalingFactors0.0910.0000.091
exoCount7.2580.0447.301
exogenousScalingFactor7.8710.0367.907
experimentList8.2370.0488.286
exportBigWigs1.8810.0041.884
extractBinding10.452 0.07610.529
getAverageBindingValues0.2660.0000.267
getBam0.2490.0080.258
getBigWigFile0.3650.0000.365
getCount0.3650.0080.373
getDatasetList0.3370.0160.353
getExoCount0.3720.0160.388
getExogenousBam0.3120.0080.319
getExogenousScalingFactor0.3680.0040.373
getExpName0.3650.0000.365
getExperimentList0.3510.0040.354
getExperimentListBigWigs0.3660.0040.371
getLoadedData0.1760.0000.175
getMatBindingValues0.4680.1000.571
getRatio0.1430.0000.147
getScalingFactor0.2590.0000.259
inputSubtraction2.5630.0042.567
matBindingValues7.7960.0567.851
plotCor0.420.000.42
plotHeatmaps0.6480.0040.652
plotProfile0.7960.0190.816
plotTransform0.8040.0040.808
scaling2.7940.0052.798
scalingFactor7.3060.0547.361
spikeDataset0.5030.0040.507
spikePipe11.465 0.07211.538
spikeSummary0.0040.0000.005