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This page was generated on 2023-04-12 11:05:00 -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 CAGEfightR on nebbiolo2


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 244/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.18.0  (landing page)
Malte Thodberg
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_16
git_last_commit: de07aac
git_last_commit_date: 2022-11-01 11:17:49 -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: CAGEfightR
Version: 1.18.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CAGEfightR_1.18.0.tar.gz
StartedAt: 2023-04-10 19:28:24 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:36:24 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 480.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CAGEfightR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.18.0’
* 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 loading without being on the library search path ... 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 5.39  1.143   5.451
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction_to_CAGEfightR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEfightR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
assignGeneID4.0350.1604.196
assignMissingID1.0580.0161.073
assignTxID0.8160.0400.855
assignTxType000
balanceBC0.0000.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0330.0000.034
bwGenomeCompatibility0.0150.0000.015
bwValid0.0060.0000.007
calcBidirectionality0.3720.0080.380
calcComposition2.3780.0762.453
calcPooled0.0950.0000.094
calcShape2.1660.1122.278
calcSupport0.1070.0000.107
calcTPM0.1190.0040.123
calcTotalTags0.0650.0000.065
checkCTSSs0.2400.0200.261
checkPeaked0.0620.0000.062
checkPooled0.0510.0000.050
clusterBidirectionally000
clusterUnidirectionally1.2580.0401.298
combineClusters0.7780.0200.797
convertBAM2BigWig000
convertBED2BigWig0.0010.0000.000
convertGRanges2GPos0.0740.0000.074
exampleDesign0.0050.0000.004
findLinks5.3901.1435.451
findStretches0.3760.0440.420
quantifyCTSSs0.0010.0000.000
quantifyCTSSs2000
quantifyClusters0.4220.0320.454
quantifyGenes1.1930.0521.245
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR000
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.3620.0240.386
subsetByComposition1.1270.0111.137
subsetBySupport0.0640.0040.068
swapRanges0.1810.0040.185
swapScores0.1060.0000.106
trackBalance000
trackCTSS3.4730.2563.729
trackClusters2.2490.0482.297
trackLinks1.0810.6651.117
trimToPeak0.7140.0520.767
trimToPercentiles1.7870.0001.787
tuneTagClustering000
utilsAggregateRows0.3160.1120.428
utilsDeStrand0.1000.0000.101
utilsScoreOverlaps0.0560.0000.056
utilsSimplifyTxDb000