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CHECK report for CAGEr on merida1

This page was generated on 2019-04-16 11:56:46 -0400 (Tue, 16 Apr 2019).

Package 191/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.24.0
Vanja Haberle , Charles Plessy
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: RELEASE_3_8
Last Commit: 420fec4
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.24.0.tar.gz
StartedAt: 2019-04-15 22:43:27 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:51:19 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 472.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.24.0’
* package encoding: UTF-8
* 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 ‘CAGEr’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
importPublicData           41.706 10.947  41.454
cumulativeCTSSdistribution 29.247  9.301  35.319
quantilePositions          30.192  0.831  29.919
distclu-functions          11.027  6.221   7.541
aggregateTagClusters       14.560  2.171  10.381
clusterCTSS                12.659  3.311  10.499
mergeCAGEsets               4.687  1.875   3.527
scoreShift                  5.488  0.035   5.561
coverage-functions          4.581  0.618   5.227
* 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

CAGEr.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CAGEr’ ...
** 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
* DONE (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class4.5030.2844.837
CAGEr_Multicore0.0320.0050.038
CAGEset-class0.0050.0010.006
CTSS-class0.0380.0040.042
CTSSclusteringMethod0.0130.0020.015
CTSScoordinates0.0580.0020.061
CTSSnormalizedTpm2.1091.9511.056
CTSStagCount0.3120.0050.324
CTSStagCountTable0.0090.0010.009
CTSStoGenes0.5310.0100.551
CustomConsensusClusters1.0960.0351.139
GeneExpDESeq21.7020.0481.776
GeneExpSE0.0060.0000.006
QuantileWidthFunctions000
aggregateTagClusters14.560 2.17110.381
annotateCTSS1.6200.0241.653
byCtss0.0140.0090.009
clusterCTSS12.659 3.31110.499
consensusClusterConvertors0.3770.0010.044
consensusClusters4.0730.5554.662
consensusClustersDESeq20.1780.0060.185
consensusClustersTpm0.0080.0010.008
coverage-functions4.5810.6185.227
cumulativeCTSSdistribution29.247 9.30135.319
distclu-functions11.027 6.221 7.541
exampleCAGEexp0.0020.0030.000
exampleCAGEset0.0700.1000.022
exportCTSStoBedGraph2.0520.0352.131
exportToBed4.3230.0134.378
expressionClasses0.0030.0000.004
extractExpressionClass0.0110.0010.012
genomeName0.0010.0000.001
getCTSS0.5370.3440.359
getExpressionProfiles1.040.640.67
getShiftingPromoters0.0070.0000.008
hanabi0.2640.0080.274
hanabiPlot0.3670.1070.483
import.CAGEscanMolecule000
import.CTSS0.0570.0010.058
import.bam000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule000
importPublicData41.70610.94741.454
inputFiles0.0020.0020.000
inputFilesType0.0010.0010.001
librarySizes0.0020.0020.000
mapStats0.6970.6800.357
mergeCAGEsets4.6871.8753.527
mergeSamples0.4280.0030.436
moleculesGR2CTSS0.1370.0010.137
normalizeTagCount3.2601.3270.757
parseCAGEscanBlocksToGrangeTSS0.0160.0010.017
plotAnnot3.3140.0163.351
plotCorrelation1.5270.0031.539
plotExpressionProfiles0.1770.0020.180
plotInterquantileWidth0.3260.0040.333
plotReverseCumulatives1.7671.2660.812
quantilePositions30.192 0.83129.919
ranges2annot0.3900.0010.392
ranges2genes0.0770.0010.077
ranges2names0.0790.0310.111
sampleLabels0.0000.0010.001
scoreShift5.4880.0355.561
seqNameTotalsSE0.0050.0000.005
setColors0.3370.0030.342
strandInvaders1.8201.4391.077
summariseChrExpr0.6610.0050.672
tagClusterConvertors0.3350.0030.339
tagClusters0.0510.0010.055