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CHECK report for CAGEr on machv2

This page was generated on 2020-10-17 11:58:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAGEr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 219/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.30.3
Vanja Haberle , Charles Plessy , Damir Baranasic , Sarvesh Nikumbh
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: RELEASE_3_11
Last Commit: 3cc7af7
Last Changed Date: 2020-07-14 02:04:27 -0400 (Tue, 14 Jul 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  WARNINGS  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: CAGEr
Version: 1.30.3
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_1.30.3.tar.gz
StartedAt: 2020-10-16 23:19:05 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:29:14 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 608.7 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_1.30.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAGEr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.30.3’
* 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 (user + system) or elapsed time > 5s
                             user system elapsed
importPublicData           42.592  1.257  50.846
cumulativeCTSSdistribution 34.186  1.938  36.177
quantilePositions          35.345  0.481  35.861
aggregateTagClusters       19.005  0.086  19.153
clusterCTSS                 9.132  0.274   9.418
distclu-functions           8.913  0.284   9.206
scoreShift                  7.193  0.033   7.230
CAGEexp-class               5.995  0.593   6.619
consensusClusters           5.886  0.261   6.161
mergeCAGEsets               5.684  0.201   5.893
coverage-functions          5.334  0.341   5.686
exportToBed                 5.000  0.015   5.018
* 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/4.0/Resources/library’
* installing *source* package ‘CAGEr’ ...
** using staged installation
** 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 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class5.9950.5936.619
CAGEr_Multicore0.8930.0120.908
CAGEset-class0.0050.0020.007
CTSS-class0.0570.0010.059
CTSSclusteringMethod0.0150.0010.016
CTSScoordinates0.1860.0020.188
CTSSnormalizedTpm1.2770.0081.285
CTSStagCount0.3750.0250.400
CTSStagCountTable0.0090.0020.010
CTSStoGenes1.1080.0061.116
CustomConsensusClusters1.8350.0071.843
GeneExpDESeq22.1400.0322.175
GeneExpSE0.0090.0010.010
QuantileWidthFunctions0.0000.0010.001
aggregateTagClusters19.005 0.08619.153
annotateCTSS2.5340.0112.548
byCtss0.0080.0010.009
clusterCTSS9.1320.2749.418
consensusClusterConvertors0.0550.0020.056
consensusClusters5.8860.2616.161
consensusClustersDESeq20.4770.0120.490
consensusClustersTpm0.0080.0000.010
coverage-functions5.3340.3415.686
cumulativeCTSSdistribution34.186 1.93836.177
distclu-functions8.9130.2849.206
exampleCAGEexp0.0010.0010.001
exampleCAGEset0.0230.0020.025
exportCTSStoBedGraph4.4890.0514.546
exportToBed5.0000.0155.018
expressionClasses0.0020.0010.003
extractExpressionClass0.0100.0020.011
genomeName0.0010.0010.001
getCTSS0.2140.0090.223
getExpressionProfiles0.6820.0030.686
getShiftingPromoters0.0050.0010.006
hanabi0.3460.0020.348
hanabiPlot0.4330.0110.446
import.CAGEscanMolecule0.0000.0010.001
import.CTSS0.1500.0030.153
import.bam0.0000.0010.001
import.bedCTSS0.0000.0010.001
import.bedScore0.0000.0000.001
import.bedmolecule0.0000.0000.001
importPublicData42.592 1.25750.846
inputFiles000
inputFilesType0.0000.0010.001
librarySizes0.0000.0000.001
mapStats0.0850.0040.089
mergeCAGEsets5.6840.2015.893
mergeSamples1.3450.0061.352
moleculesGR2CTSS0.2450.0010.246
normalizeTagCount1.0680.0051.074
parseCAGEscanBlocksToGrangeTSS0.0390.0010.041
plotAnnot3.1550.0303.191
plotCorrelation0.8240.0030.830
plotExpressionProfiles0.2360.0050.242
plotInterquantileWidth1.1420.0071.155
plotReverseCumulatives0.8960.0060.905
quantilePositions35.345 0.48135.861
ranges2annot0.6640.0030.667
ranges2genes0.1110.0000.112
ranges2names0.0690.0010.070
sampleLabels0.0000.0010.001
scoreShift7.1930.0337.230
seqNameTotalsSE0.0070.0010.008
setColors2.5840.0082.595
strandInvaders1.6570.0831.749
summariseChrExpr0.8980.0040.903
tagClusterConvertors0.5580.0110.569
tagClusters0.0950.0070.103