Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:05:17 -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 CAGEfightR on nebbiolo1


To the developers/maintainers of the CAGEfightR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.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 241/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.16.0  (landing page)
Malte Thodberg
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_15
git_last_commit: 86ba129
git_last_commit_date: 2022-04-26 11:49:10 -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: CAGEfightR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CAGEfightR_1.16.0.tar.gz
StartedAt: 2022-05-17 18:41:39 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 18:47:03 -0400 (Tue, 17 May 2022)
EllapsedTime: 324.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CAGEfightR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.16.0’
* 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 ‘CAGEfightR’ 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
findLinks 4.356  1.036   4.439
* 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

CAGEfightR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CAGEfightR’ ...
** 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 (CAGEfightR)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID3.7230.1133.835
assignMissingID1.0980.0321.130
assignTxID0.8540.0080.862
assignTxType0.0010.0000.001
balanceBC0.0010.0000.001
balanceD0.0010.0000.001
bwCommonGenome0.0310.0040.039
bwGenomeCompatibility0.0160.0000.017
bwValid0.0050.0040.007
calcBidirectionality0.4440.0040.447
calcComposition1.2920.0201.312
calcPooled0.1020.0000.102
calcShape3.1940.2123.405
calcSupport0.0940.0160.110
calcTPM0.1170.0120.129
calcTotalTags0.0570.0070.064
checkCTSSs0.2250.0120.237
checkPeaked0.0510.0080.060
checkPooled0.0520.0040.056
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally1.1650.0261.192
combineClusters0.7250.0240.749
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0750.0040.079
exampleDesign0.0020.0020.005
findLinks4.3561.0364.439
findStretches0.3620.0480.410
quantifyCTSSs0.0010.0000.001
quantifyCTSSs20.0010.0000.001
quantifyClusters0.400.040.44
quantifyGenes1.2090.0521.261
quickEnhancers0.0010.0000.000
quickGenes0.0000.0000.001
quickTSSs000
shapeEntropy000
shapeIQR0.0000.0000.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.3640.0050.369
subsetByComposition1.1670.0401.207
subsetBySupport0.070.000.07
swapRanges0.1850.0040.189
swapScores0.110.000.11
trackBalance0.0010.0000.000
trackCTSS3.0190.2123.231
trackClusters2.2000.0362.236
trackLinks1.1600.6861.194
trimToPeak0.7460.0800.826
trimToPercentiles1.7160.0121.728
tuneTagClustering000
utilsAggregateRows0.3770.5120.889
utilsDeStrand0.1070.0000.107
utilsScoreOverlaps0.0570.0000.058
utilsSimplifyTxDb0.0010.0000.000