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CHECK report for ChIPSeqSpike on malbec2

This page was generated on 2019-10-16 12:13:12 -0400 (Wed, 16 Oct 2019).

Package 265/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPSeqSpike 1.4.0
Nicolas Descostes
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ChIPSeqSpike
Branch: RELEASE_3_9
Last Commit: 2791b92
Last Changed Date: 2019-05-02 11:54:10 -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  OK  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: ChIPSeqSpike
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.4.0.tar.gz
StartedAt: 2019-10-16 00:28:12 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:34:39 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 387.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPSeqSpike.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIPSeqSpike.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 ‘ChIPSeqSpike/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPSeqSpike’ version ‘1.4.0’
* 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 or elapsed time > 5s
                         user system elapsed
spikePipe              11.920  0.108  12.038
averageBindingValues   11.004  0.319  13.800
exogenousScalingFactor  9.633  0.084   9.718
experimentList          9.136  0.076   9.214
bigWigFile              9.124  0.056   9.195
exoCount                8.655  0.068   8.732
count                   8.177  0.068   8.333
extractBinding          7.813  0.044   7.858
scalingFactor           7.807  0.028   7.861
matBindingValues        6.766  0.104   6.882
* 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-3.9-bioc/R/bin/R CMD INSTALL ChIPSeqSpike
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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 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("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 
 13.407   0.577  13.974 

Example timings

ChIPSeqSpike.Rcheck/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class0.0160.0000.016
ChIPSeqSpikeDatasetBoost-class0.4340.0160.502
ChIPSeqSpikeDatasetList-class0.0460.0000.124
ChIPSeqSpikeDatasetListBoost-class0.4760.0120.706
Experiment-class0.0020.0000.002
ExperimentLoaded-class0.0670.0040.072
averageBindingValues11.004 0.31913.800
bigWigFile9.1240.0569.195
boxplotSpike2.4840.0082.506
count8.1770.0688.333
datasetList0.3250.0000.325
estimateScalingFactors0.1030.0000.103
exoCount8.6550.0688.732
exogenousScalingFactor9.6330.0849.718
experimentList9.1360.0769.214
exportBigWigs0.9360.0040.940
extractBinding7.8130.0447.858
getAverageBindingValues0.3730.0040.377
getBam0.2830.0080.291
getBigWigFile0.2440.0160.260
getCount0.2580.0000.258
getDatasetList0.270.000.27
getExoCount0.2550.0000.255
getExogenousBam0.260.000.26
getExogenousScalingFactor0.2630.0040.267
getExpName0.2510.0120.263
getExperimentList0.2550.0040.259
getExperimentListBigWigs0.2570.0000.257
getLoadedData0.0930.0000.093
getMatBindingValues0.4300.0640.498
getRatio0.1050.0000.106
getScalingFactor0.2770.0040.282
inputSubtraction1.3380.0041.342
matBindingValues6.7660.1046.882
plotCor0.5710.0080.579
plotHeatmaps0.9060.0120.918
plotProfile0.7860.0120.798
plotTransform0.6310.0040.636
scaling1.4890.0081.497
scalingFactor7.8070.0287.861
spikeDataset0.5140.0000.515
spikePipe11.920 0.10812.038
spikeSummary0.0040.0000.004