Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-22 11:05:59 -0400 (Wed, 22 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4271
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4214
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4259
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 lconway


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? 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 246/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.4.0  (landing page)
Charles Plessy
Snapshot Date: 2023-03-20 14:00:04 -0400 (Mon, 20 Mar 2023)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_16
git_last_commit: 4ce371f
git_last_commit_date: 2022-11-01 11:07:54 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.4.0
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_2.4.0.tar.gz
StartedAt: 2023-03-20 19:29:47 -0400 (Mon, 20 Mar 2023)
EndedAt: 2023-03-20 19:36:21 -0400 (Mon, 20 Mar 2023)
EllapsedTime: 394.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running 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_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CAGEr.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘2.4.0’
* 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 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
cumulativeCTSSdistribution 29.395  2.176  31.629
clusterCTSS                26.278  0.270  26.627
exportToTrack              24.612  0.183  24.840
quantilePositions          15.199  0.069  15.313
aggregateTagClusters        5.665  0.036   5.710
* 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/4.2/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-class2.7290.6024.085
CAGEr_Multicore0.8720.0060.880
CTSS-class0.2760.0070.311
CTSSclusteringMethod0.0000.0000.001
CTSScoordinates0.0620.0030.130
CTSSnormalizedTpm0.6280.0430.704
CTSStagCount0.7620.0480.841
CTSStoGenes0.3390.0020.342
CustomConsensusClusters0.8610.0050.868
GeneExpDESeq20.9630.0260.991
GeneExpSE0.0030.0000.004
QuantileWidthFunctions0.0970.0010.099
aggregateTagClusters5.6650.0365.710
annotateCTSS1.3720.0091.385
byCtss0.0040.0000.004
clusterCTSS26.278 0.27026.627
consensusClusters0.0980.0010.099
consensusClustersDESeq20.1730.0010.174
consensusClustersTpm0.0040.0000.005
coverage-functions3.4050.2253.650
cumulativeCTSSdistribution29.395 2.17631.629
distclu-functions3.3210.1593.488
exampleCAGEexp0.0010.0010.000
exportToTrack24.612 0.18324.840
expressionClasses0.0120.0000.013
genomeName0.0000.0000.001
getCTSS0.9470.0120.978
getExpressionProfiles1.9700.0111.984
getShiftingPromoters000
hanabi0.1870.0040.192
hanabiPlot0.2700.0200.292
import.CAGEscanMolecule000
import.CTSS0.060.000.06
import.bam000
import.bedCTSS0.0010.0000.000
import.bedScore000
import.bedmolecule0.0000.0000.001
inputFiles0.0010.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0000.0000.001
mapStats0.0380.0010.039
mergeCAGEsets1.9880.0182.011
mergeSamples0.4850.0040.491
moleculesGR2CTSS0.1280.0010.130
normalizeTagCount0.4280.0020.432
parseCAGEscanBlocksToGrangeTSS0.0170.0000.017
plotAnnot2.3880.0572.457
plotCorrelation0.2530.0040.258
plotExpressionProfiles4.0760.1304.217
plotInterquantileWidth1.8490.0081.861
plotReverseCumulatives0.3370.0050.344
quantilePositions15.199 0.06915.313
ranges2annot0.3500.0040.356
ranges2genes0.0460.0010.047
ranges2names0.0430.0000.043
sampleLabels0.0050.0010.006
scoreShift000
seqNameTotalsSE0.0050.0010.006
setColors0.4380.0050.463
strandInvaders0.6610.0860.774
summariseChrExpr0.4840.0030.489
tagClusters0.0920.0030.096