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This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 264/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.26.0  (landing page)
Malte Thodberg
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_20
git_last_commit: 3f0d403
git_last_commit_date: 2024-10-29 10:28:27 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for CAGEfightR on lconway

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2024-11-19 20:12:40 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 20:21:47 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 547.0 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 4.973  0.658   5.227
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-x86_64/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
assignGeneID2.9920.0913.116
assignMissingID0.8520.0330.887
assignTxID0.7530.0270.783
assignTxType0.0000.0010.001
balanceBC0.0010.0000.000
balanceD000
bwCommonGenome0.0310.0040.037
bwGenomeCompatibility0.0150.0020.017
bwValid0.0070.0020.010
calcBidirectionality0.3530.0110.366
calcComposition1.1030.0301.136
calcPooled0.0710.0050.077
calcShape2.7590.1492.912
calcSupport0.0770.0020.079
calcTPM0.1010.0030.104
calcTotalTags0.0500.0020.052
checkCTSSs0.2040.0060.225
checkPeaked0.0510.0040.055
checkPooled0.0500.0020.052
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally1.1160.0321.155
combineClusters0.6150.0090.627
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0570.0010.057
exampleDesign0.0030.0070.010
findLinks4.9730.6585.227
findStretches0.3080.0480.357
quantifyCTSSs0.0000.0010.000
quantifyCTSSs2000
quantifyClusters0.3290.0380.369
quantifyGenes1.0620.0991.165
quickEnhancers0.0000.0010.000
quickGenes0.0010.0000.000
quickTSSs000
shapeEntropy0.0010.0000.000
shapeIQR0.0010.0000.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.3530.0330.387
subsetByComposition0.9750.0361.014
subsetBySupport0.0530.0040.057
swapRanges0.1380.0060.144
swapScores0.0760.0040.081
trackBalance0.0000.0010.001
trackCTSS2.7030.1782.890
trackClusters1.7770.0261.808
trackLinks0.7880.3550.964
trimToPeak0.6440.0740.720
trimToPercentiles1.4300.0281.461
tuneTagClustering0.0000.0010.000
utilsAggregateRows0.2960.3280.631
utilsDeStrand0.1010.0030.104
utilsScoreOverlaps0.0570.0010.058
utilsSimplifyTxDb0.0000.0000.001