Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:06:26 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 palomino3


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 243/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.2.0  (landing page)
Charles Plessy
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_15
git_last_commit: 74d9a97
git_last_commit_date: 2022-04-26 11:13:41 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.2.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CAGEr_2.2.0.tar.gz
StartedAt: 2022-05-17 22:20:47 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 22:28:59 -0400 (Tue, 17 May 2022)
EllapsedTime: 492.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CAGEr_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/CAGEr.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '2.2.0'
* 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 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 40.61   2.53   43.14
clusterCTSS                37.98   0.59   38.61
exportToTrack              32.92   0.33   33.27
quantilePositions          20.84   0.22   21.08
aggregateTagClusters        8.94   0.11    9.04
CAGEexp-class               5.15   0.78    6.05
plotExpressionProfiles      5.49   0.27    5.75
coverage-functions          4.87   0.14    5.02
strandInvaders              0.83   0.16    5.09
* 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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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-class5.150.786.05
CAGEr_Multicore0.070.000.08
CTSS-class0.250.020.27
CTSSclusteringMethod000
CTSScoordinates0.100.000.09
CTSSnormalizedTpm0.680.000.69
CTSStagCount0.790.030.81
CTSStoGenes0.400.000.41
CustomConsensusClusters1.170.001.17
GeneExpDESeq21.440.051.49
GeneExpSE0.020.000.01
QuantileWidthFunctions0.120.030.16
aggregateTagClusters8.940.119.04
annotateCTSS1.750.031.79
byCtss0.020.000.01
clusterCTSS37.98 0.5938.61
consensusClusters0.20.00.2
consensusClustersDESeq20.250.000.25
consensusClustersTpm0.020.000.02
coverage-functions4.870.145.02
cumulativeCTSSdistribution40.61 2.5343.14
distclu-functions4.460.224.67
exampleCAGEexp000
exportToTrack32.92 0.3333.27
expressionClasses0.010.000.01
genomeName000
getCTSS1.220.001.22
getExpressionProfiles2.300.022.32
getShiftingPromoters000
hanabi0.250.010.26
hanabiPlot0.420.030.45
import.CAGEscanMolecule000
import.CTSS0.080.000.08
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles000
inputFilesType000
librarySizes000
mapStats0.050.000.05
mergeCAGEsets2.840.002.84
mergeSamples0.610.010.62
moleculesGR2CTSS0.120.000.14
normalizeTagCount0.750.020.77
parseCAGEscanBlocksToGrangeTSS0.040.000.03
plotAnnot2.950.032.98
plotCorrelation0.370.010.37
plotExpressionProfiles5.490.275.75
plotInterquantileWidth2.950.032.99
plotReverseCumulatives0.490.000.48
quantilePositions20.84 0.2221.08
ranges2annot0.340.010.36
ranges2genes0.070.000.06
ranges2names0.090.000.09
sampleLabels0.010.000.02
scoreShift000
seqNameTotalsSE000
setColors0.440.000.44
strandInvaders0.830.165.09
summariseChrExpr0.530.020.55
tagClusters0.170.000.17