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This page was generated on 2022-06-24 12:07:09 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 merida1


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: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.16.0.tar.gz
StartedAt: 2022-06-24 00:18:14 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:28:35 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 620.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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    6.420  1.813   6.775
assignGeneID 6.187  0.166   6.457
calcShape    5.945  0.223   6.245
trackCTSS    5.624  0.259   5.959
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
assignGeneID6.1870.1666.457
assignMissingID2.0220.0362.062
assignTxID1.7310.0261.760
assignTxType0.0010.0010.000
balanceBC0.0010.0000.000
balanceD0.0000.0000.001
bwCommonGenome0.0680.0050.074
bwGenomeCompatibility0.0340.0040.039
bwValid0.0150.0040.018
calcBidirectionality0.9030.0170.923
calcComposition3.6780.0543.763
calcPooled0.2570.0250.284
calcShape5.9450.2236.245
calcSupport0.2300.0050.236
calcTPM0.2590.0050.265
calcTotalTags0.1260.0040.130
checkCTSSs0.5250.0060.536
checkPeaked0.1250.0030.129
checkPooled0.1140.0040.119
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally2.8250.0252.856
combineClusters1.4440.0241.468
convertBAM2BigWig000
convertBED2BigWig0.0000.0000.001
convertGRanges2GPos0.1490.0010.150
exampleDesign0.0090.0110.019
findLinks6.4201.8136.775
findStretches0.9060.1011.120
quantifyCTSSs0.0000.0010.001
quantifyCTSSs20.0010.0000.001
quantifyClusters0.8710.0831.038
quantifyGenes2.5610.1523.028
quickEnhancers0.0000.0000.001
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0010.001
shapeMean0.0010.0000.001
shapeMultimodality0.0000.0000.001
subsetByBidirectionality0.8800.0640.982
subsetByComposition2.5010.0552.587
subsetBySupport0.1670.0040.179
swapRanges0.3400.0090.366
swapScores0.2280.0090.245
trackBalance0.0010.0000.001
trackCTSS5.6240.2595.959
trackClusters3.2710.0253.325
trackLinks2.3531.0872.428
trimToPeak1.6910.1581.858
trimToPercentiles4.2710.0584.392
tuneTagClustering000
utilsAggregateRows0.7740.3621.153
utilsDeStrand0.2540.0040.259
utilsScoreOverlaps0.1450.0010.147
utilsSimplifyTxDb0.0010.0010.000