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CHECK report for ChIPSeqSpike on malbec2

This page was generated on 2018-10-17 08:31:13 -0400 (Wed, 17 Oct 2018).

Package 236/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPSeqSpike 1.0.0
Nicolas Descostes
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIPSeqSpike
Branch: RELEASE_3_7
Last Commit: 6af62ac
Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPSeqSpike
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.0.0.tar.gz
StartedAt: 2018-10-15 23:12:18 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:17:17 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 298.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPSeqSpike.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIPSeqSpike_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ChIPSeqSpike.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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              12.568  0.124  12.714
averageBindingValues   10.172  0.132  10.351
extractBinding          8.812  0.132   8.959
experimentList          8.624  0.112   8.748
exoCount                8.440  0.108   8.568
scalingFactor           8.392  0.080   8.483
count                   8.372  0.092   8.478
exogenousScalingFactor  8.372  0.084   8.471
matBindingValues        8.240  0.092   8.345
bigWigFile              8.056  0.112   8.176
* 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-3.7-bioc/R/bin/R CMD INSTALL ChIPSeqSpike
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ChIPSeqSpike’ ...
** 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
* DONE (ChIPSeqSpike)

Tests output

ChIPSeqSpike.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 
 10.372   0.416  10.800 

Example timings

ChIPSeqSpike.Rcheck/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class0.0080.0000.009
ChIPSeqSpikeDatasetBoost-class0.2280.0040.259
ChIPSeqSpikeDatasetList-class0.0200.0040.023
ChIPSeqSpikeDatasetListBoost-class0.3240.0040.328
Experiment-class0.0000.0000.001
ExperimentLoaded-class0.0440.0000.047
averageBindingValues10.172 0.13210.351
bigWigFile8.0560.1128.176
boxplotSpike1.2600.0121.271
count8.3720.0928.478
datasetList0.2600.0000.263
estimateScalingFactors0.0800.0080.091
exoCount8.4400.1088.568
exogenousScalingFactor8.3720.0848.471
experimentList8.6240.1128.748
exportBigWigs0.7440.0080.756
extractBinding8.8120.1328.959
getAverageBindingValues0.2760.0040.281
getBam0.2960.0000.295
getBigWigFile0.2600.0040.264
getCount0.2720.0040.274
getDatasetList0.2680.0000.267
getExoCount0.2720.0000.275
getExogenousBam0.2640.0080.273
getExogenousScalingFactor0.2560.0080.265
getExpName0.9120.0120.927
getExperimentList0.2560.0080.263
getExperimentListBigWigs0.2600.0040.265
getLoadedData0.1000.0000.102
getMatBindingValues0.3440.0760.418
getRatio0.1200.0000.118
getScalingFactor0.2560.0040.261
inputSubtraction0.8760.0040.879
matBindingValues8.2400.0928.345
plotCor0.3920.0080.400
plotHeatmaps0.5800.0080.590
plotProfile0.5120.0120.523
plotTransform0.5640.0120.575
scaling1.3280.0121.340
scalingFactor8.3920.0808.483
spikeDataset0.3440.0000.345
spikePipe12.568 0.12412.714
spikeSummary0.0080.0000.006