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CHECK report for ChIPSeqSpike on merida2

This page was generated on 2018-10-17 08:59:29 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPSeqSpike_1.0.0.tar.gz
StartedAt: 2018-10-16 20:25:21 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:32:29 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 428.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPSeqSpike.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPSeqSpike.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPSeqSpike_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPSeqSpike.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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              14.787  0.605  15.496
averageBindingValues   14.648  0.702  15.515
exoCount               12.263  0.434  12.811
extractBinding         12.124  0.436  12.672
experimentList         11.957  0.493  12.549
count                  11.840  0.476  12.414
bigWigFile             11.788  0.462  12.365
exogenousScalingFactor 11.594  0.444  12.169
matBindingValues       11.412  0.456  11.974
scalingFactor          11.045  0.431  11.603
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPSeqSpike
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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-apple-darwin15.6.0 (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 
 13.416   0.729  14.236 

Example timings

ChIPSeqSpike.Rcheck/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class0.0190.0020.020
ChIPSeqSpikeDatasetBoost-class0.3530.0030.359
ChIPSeqSpikeDatasetList-class0.0420.0030.045
ChIPSeqSpikeDatasetListBoost-class0.5120.0120.533
Experiment-class0.0030.0000.003
ExperimentLoaded-class0.0650.0030.070
averageBindingValues14.648 0.70215.515
bigWigFile11.788 0.46212.365
boxplotSpike1.8090.0611.896
count11.840 0.47612.414
datasetList0.3200.0130.339
estimateScalingFactors0.1280.0020.131
exoCount12.263 0.43412.811
exogenousScalingFactor11.594 0.44412.169
experimentList11.957 0.49312.549
exportBigWigs1.1000.0131.128
extractBinding12.124 0.43612.672
getAverageBindingValues0.3420.0160.359
getBam0.3250.0160.344
getBigWigFile0.3160.0140.330
getCount0.3100.0160.330
getDatasetList0.3050.0140.321
getExoCount0.2890.0140.306
getExogenousBam0.3050.0130.321
getExogenousScalingFactor0.2940.0150.318
getExpName0.3120.0140.328
getExperimentList0.3050.0170.323
getExperimentListBigWigs0.3240.0150.346
getLoadedData0.1390.0020.143
getMatBindingValues0.4490.1790.633
getRatio0.1660.0140.182
getScalingFactor0.2580.0110.270
inputSubtraction1.1460.0221.180
matBindingValues11.412 0.45611.974
plotCor0.5210.0170.543
plotHeatmaps0.6810.0210.720
plotProfile0.6290.0130.664
plotTransform0.6810.0270.716
scaling1.8950.0261.944
scalingFactor11.045 0.43111.603
spikeDataset0.5190.0070.537
spikePipe14.787 0.60515.496
spikeSummary0.0050.0010.007