Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:07:45 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CAGEr on machv2


To the developers/maintainers of the CAGEr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 237/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.0.2  (landing page)
Charles Plessy
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_14
git_last_commit: 9218aa9
git_last_commit_date: 2021-11-16 19:37:08 -0500 (Tue, 16 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.0.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.0.2.tar.gz
StartedAt: 2022-01-18 10:53:06 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 11:04:12 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 666.4 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/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.0.2’
* 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 LazyData ... 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
clusterCTSS                63.448  0.607  64.127
exportToTrack              58.348  0.168  58.562
cumulativeCTSSdistribution 33.992  1.785  35.812
quantilePositions          29.928  0.303  30.259
aggregateTagClusters       15.551  0.048  15.611
plotExpressionProfiles      7.282  0.180   7.469
CAGEexp-class               5.995  0.628   6.635
distclu-functions           6.019  0.292   6.314
plotInterquantileWidth      5.176  0.009   5.189
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-class5.9950.6286.635
CAGEr_Multicore0.9410.0190.960
CTSS-class0.4950.0020.497
CTSSclusteringMethod0.0010.0010.001
CTSScoordinates0.1610.0030.165
CTSSnormalizedTpm1.3330.0421.376
CTSStagCount1.2870.0151.303
CTSStoGenes1.0050.0031.009
CustomConsensusClusters2.1740.0082.182
GeneExpDESeq22.2170.0372.256
GeneExpSE0.0210.0010.021
QuantileWidthFunctions0.2510.0020.252
aggregateTagClusters15.551 0.04815.611
annotateCTSS3.8250.0123.845
byCtss0.0080.0000.009
clusterCTSS63.448 0.60764.127
consensusClusters0.3490.0030.352
consensusClustersDESeq20.6210.0020.623
consensusClustersTpm0.0160.0010.016
coverage-functions3.5270.2633.792
cumulativeCTSSdistribution33.992 1.78535.812
distclu-functions6.0190.2926.314
exampleCAGEexp0.0010.0010.000
exportToTrack58.348 0.16858.562
expressionClasses0.0560.0010.057
genomeName0.0010.0010.001
getCTSS2.0440.0172.060
getExpressionProfiles4.4940.0254.524
getShiftingPromoters0.0000.0010.001
hanabi0.4300.0050.435
hanabiPlot0.4870.0180.509
import.CAGEscanMolecule0.0000.0010.000
import.CTSS0.1940.0020.197
import.bam0.0000.0000.001
import.bedCTSS000
import.bedScore0.0010.0010.000
import.bedmolecule0.0010.0000.000
inputFiles0.0010.0000.001
inputFilesType0.0010.0010.001
librarySizes0.0000.0000.001
mapStats0.0710.0020.073
mergeCAGEsets4.6900.0244.718
mergeSamples1.3170.0051.322
moleculesGR2CTSS0.2580.0010.260
normalizeTagCount1.4170.0031.422
parseCAGEscanBlocksToGrangeTSS0.0850.0020.086
plotAnnot2.8740.0222.900
plotCorrelation0.7490.0030.753
plotExpressionProfiles7.2820.1807.469
plotInterquantileWidth5.1760.0095.189
plotReverseCumulatives0.6450.0040.650
quantilePositions29.928 0.30330.259
ranges2annot0.6230.0020.626
ranges2genes0.0820.0000.082
ranges2names0.1050.0000.105
sampleLabels0.0020.0010.003
scoreShift0.0010.0010.000
seqNameTotalsSE0.0140.0010.016
setColors0.8870.0060.894
strandInvaders1.4600.0721.542
summariseChrExpr1.1050.0031.109
tagClusters0.2560.0040.261