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CHECK report for CAGEr on malbec1

This page was generated on 2020-08-07 11:19:12 -0400 (Fri, 07 Aug 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 214/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.31.4
Vanja Haberle , Charles Plessy , Damir Baranasic , Sarvesh Nikumbh
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: master
Last Commit: f845b5c
Last Changed Date: 2020-07-14 02:01:55 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.31.4
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAGEr_1.31.4.tar.gz
StartedAt: 2020-08-06 23:55:39 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-07 00:03:34 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 474.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAGEr_1.31.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CAGEr.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.31.4’
* 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           34.988  0.500  38.704
cumulativeCTSSdistribution 30.588  4.408  35.037
quantilePositions          25.640  0.712  26.387
aggregateTagClusters       16.440  0.020  16.127
distclu-functions           7.496  0.684   8.199
clusterCTSS                 6.896  0.296   7.189
scoreShift                  6.832  0.016   6.861
CAGEexp-class               5.856  0.244   6.142
consensusClusters           5.164  0.496   5.678
coverage-functions          4.868  0.436   5.320
plotReverseCumulatives      5.100  0.016   1.522
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-class5.8560.2446.142
CAGEr_Multicore1.0000.1921.196
CAGEset-class0.0000.0000.002
CTSS-class0.0480.0000.048
CTSSclusteringMethod0.0120.0000.014
CTSScoordinates0.1400.0000.143
CTSSnormalizedTpm3.3920.0161.506
CTSStagCount0.4440.0000.443
CTSStagCountTable0.0120.0000.011
CTSStoGenes1.0720.0041.077
CustomConsensusClusters1.5320.0001.533
GeneExpDESeq21.8760.0121.898
GeneExpSE0.0080.0000.009
QuantileWidthFunctions000
aggregateTagClusters16.440 0.02016.127
annotateCTSS2.2320.0002.235
byCtss0.0040.0000.005
clusterCTSS6.8960.2967.189
consensusClusterConvertors0.0520.0040.058
consensusClusters5.1640.4965.678
consensusClustersDESeq20.2960.0000.297
consensusClustersTpm0.0080.0000.006
coverage-functions4.8680.4365.320
cumulativeCTSSdistribution30.588 4.40835.037
distclu-functions7.4960.6848.199
exampleCAGEexp0.0040.0000.000
exampleCAGEset0.0120.0000.012
exportCTSStoBedGraph2.9480.0082.959
exportToBed2.9440.0202.967
expressionClasses0.0040.0000.002
extractExpressionClass0.0080.0000.008
genomeName0.0000.0000.001
getCTSS1.6000.0080.371
getExpressionProfiles0.2720.0000.270
getShiftingPromoters0.0080.0000.007
hanabi0.4160.0040.420
hanabiPlot0.4160.0040.421
import.CAGEscanMolecule000
import.CTSS0.1120.0000.112
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData34.988 0.50038.704
inputFiles000
inputFilesType000
librarySizes000
mapStats0.0640.0000.065
mergeCAGEsets4.9320.0004.178
mergeSamples0.9040.0000.907
moleculesGR2CTSS0.140.000.14
normalizeTagCount3.1840.0081.649
parseCAGEscanBlocksToGrangeTSS0.0400.0000.039
plotAnnot2.7760.0042.787
plotCorrelation0.5640.0040.569
plotExpressionProfiles0.1480.0040.155
plotInterquantileWidth1.0360.0001.033
plotReverseCumulatives5.1000.0161.522
quantilePositions25.640 0.71226.387
ranges2annot0.5160.0000.517
ranges2genes0.0640.0000.063
ranges2names0.0560.0000.056
sampleLabels0.0040.0000.000
scoreShift6.8320.0166.861
seqNameTotalsSE0.0040.0000.008
setColors2.6800.0002.689
strandInvaders1.6320.0361.551
summariseChrExpr0.90.00.9
tagClusterConvertors0.3280.0000.328
tagClusters0.0480.0000.049