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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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

Package 259/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.25.0  (landing page)
Malte Thodberg
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: devel
git_last_commit: 28828d6
git_last_commit_date: 2024-04-30 11:06:32 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CAGEfightR on nebbiolo2

To the developers/maintainers of the CAGEfightR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CAGEfightR
Version: 1.25.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CAGEfightR_1.25.0.tar.gz
StartedAt: 2024-06-20 21:18:12 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 21:27:09 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 537.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CAGEfightR_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.25.0’
* 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 code 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 whether startup messages can be suppressed ... 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 5.593   0.98   6.023
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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
assignGeneID3.4090.0513.461
assignMissingID0.9470.0040.951
assignTxID0.7400.0070.748
assignTxType0.0010.0000.000
balanceBC000
balanceD000
bwCommonGenome0.0350.0000.036
bwGenomeCompatibility0.0160.0000.016
bwValid0.0070.0000.007
calcBidirectionality0.3750.0000.375
calcComposition1.1810.0391.221
calcPooled1.1370.1291.265
calcShape2.0050.1152.121
calcSupport0.0910.0040.095
calcTPM0.1090.0000.109
calcTotalTags0.0440.0120.056
checkCTSSs0.2060.0110.219
checkPeaked0.0480.0080.057
checkPooled0.0480.0070.056
clusterBidirectionally000
clusterUnidirectionally1.1360.0201.156
combineClusters0.7010.0120.714
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0610.0030.066
exampleDesign0.0030.0010.004
findLinks5.5930.9806.023
findStretches0.3420.0320.374
quantifyCTSSs0.0010.0000.001
quantifyCTSSs2000
quantifyClusters0.3580.0520.410
quantifyGenes1.0510.1441.195
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0000.0010.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.3810.0410.422
subsetByComposition1.0830.0641.147
subsetBySupport0.0620.0080.070
swapRanges0.1580.0160.174
swapScores0.0850.0040.090
trackBalance000
trackCTSS2.9050.4763.380
trackClusters1.9180.2362.154
trackLinks0.8190.4780.975
trimToPeak0.6830.1320.815
trimToPercentiles1.6840.1521.836
tuneTagClustering0.0010.0000.000
utilsAggregateRows0.3160.1040.420
utilsDeStrand0.1050.0120.117
utilsScoreOverlaps0.0620.0000.063
utilsSimplifyTxDb000