Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:01 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 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    OK  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: 2023-04-10 19:12:16 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:18:46 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 389.7 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 31.863  2.397  34.369
clusterCTSS                25.905  0.299  26.268
exportToTrack              23.591  0.167  23.785
quantilePositions          15.837  0.081  15.981
aggregateTagClusters        5.850  0.039   5.905
* 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-class3.2260.7133.960
CAGEr_Multicore0.8940.0070.903
CTSS-class0.2350.0030.237
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0640.0020.065
CTSSnormalizedTpm0.6180.0390.658
CTSStagCount0.6830.0370.722
CTSStoGenes0.3390.0020.341
CustomConsensusClusters0.9490.0080.959
GeneExpDESeq21.0600.0271.089
GeneExpSE0.0050.0000.005
QuantileWidthFunctions0.1140.0020.140
aggregateTagClusters5.8500.0395.905
annotateCTSS1.5000.0111.516
byCtss0.0040.0000.004
clusterCTSS25.905 0.29926.268
consensusClusters0.1090.0010.110
consensusClustersDESeq20.1340.0010.135
consensusClustersTpm0.0050.0000.008
coverage-functions3.6480.2303.894
cumulativeCTSSdistribution31.863 2.39734.369
distclu-functions3.2250.1663.398
exampleCAGEexp0.0000.0000.001
exportToTrack23.591 0.16723.785
expressionClasses0.0150.0010.014
genomeName0.0000.0010.001
getCTSS0.9500.0130.966
getExpressionProfiles2.0700.0152.091
getShiftingPromoters0.0000.0010.000
hanabi0.1720.0080.180
hanabiPlot0.2680.0150.284
import.CAGEscanMolecule000
import.CTSS0.0740.0010.075
import.bam000
import.bedCTSS000
import.bedScore0.0000.0000.001
import.bedmolecule000
inputFiles0.0020.0000.002
inputFilesType0.0010.0010.002
librarySizes0.0010.0000.001
mapStats0.0420.0020.044
mergeCAGEsets1.9330.0191.955
mergeSamples0.4520.0020.455
moleculesGR2CTSS0.1320.0010.134
normalizeTagCount0.4340.0020.437
parseCAGEscanBlocksToGrangeTSS0.0240.0000.024
plotAnnot2.3490.0532.409
plotCorrelation0.2300.0020.234
plotExpressionProfiles4.0050.1174.131
plotInterquantileWidth1.7590.0081.772
plotReverseCumulatives0.2850.0040.290
quantilePositions15.837 0.08115.981
ranges2annot0.3410.0020.344
ranges2genes0.0530.0000.052
ranges2names0.0480.0000.048
sampleLabels0.0030.0010.004
scoreShift000
seqNameTotalsSE0.0030.0010.003
setColors0.4020.0040.408
strandInvaders0.6080.0600.685
summariseChrExpr0.4080.0020.410
tagClusters0.1030.0020.105