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This page was generated on 2023-02-06 11:06:28 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 240/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.19.0  (landing page)
Malte Thodberg
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: master
git_last_commit: 8b947db
git_last_commit_date: 2022-11-01 11:17:49 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2023-02-05 23:08:07 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 23:21:54 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 827.6 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/CAGEfightR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.19.0’
* 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         8.222  0.909  10.710
calcShape         5.900  0.276   8.040
trackCTSS         5.631  0.297   7.907
assignGeneID      5.206  0.145   7.083
trimToPercentiles 4.231  0.080   5.695
* 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/4.3/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
assignGeneID5.2060.1457.083
assignMissingID3.1720.0244.194
assignTxID1.6440.0302.164
assignTxType0.0010.0010.001
balanceBC0.0000.0000.001
balanceD0.0010.0000.004
bwCommonGenome0.0740.0070.134
bwGenomeCompatibility0.0330.0040.043
bwValid0.0160.0030.021
calcBidirectionality0.9080.0171.315
calcComposition2.7310.0393.690
calcPooled0.2000.0040.275
calcShape5.9000.2768.040
calcSupport0.2200.0040.279
calcTPM0.2560.0070.329
calcTotalTags0.1190.0030.161
checkCTSSs0.5650.0110.748
checkPeaked0.1180.0030.166
checkPooled0.1140.0040.158
clusterBidirectionally000
clusterUnidirectionally2.8130.0183.727
combineClusters1.5650.0122.029
convertBAM2BigWig0.0000.0000.001
convertBED2BigWig0.0000.0000.001
convertGRanges2GPos0.1550.0010.202
exampleDesign0.0070.0130.027
findLinks 8.222 0.90910.710
findStretches0.8580.1011.278
quantifyCTSSs0.0000.0010.001
quantifyCTSSs20.0010.0010.001
quantifyClusters0.8120.0741.187
quantifyGenes2.4470.1863.472
quickEnhancers0.0010.0000.000
quickGenes0.0000.0000.001
quickTSSs000
shapeEntropy0.0010.0010.001
shapeIQR0.0010.0000.001
shapeMean0.0000.0000.001
shapeMultimodality0.0010.0000.000
subsetByBidirectionality0.8670.0471.198
subsetByComposition2.4400.0483.375
subsetBySupport0.1630.0060.227
swapRanges0.3360.0100.461
swapScores0.2200.0070.293
trackBalance0.0010.0000.001
trackCTSS5.6310.2977.907
trackClusters3.3710.0284.500
trackLinks1.9830.4202.793
trimToPeak1.680.162.41
trimToPercentiles4.2310.0805.695
tuneTagClustering0.0000.0000.001
utilsAggregateRows0.6930.3481.341
utilsDeStrand0.2430.0040.320
utilsScoreOverlaps0.1420.0010.199
utilsSimplifyTxDb0.0000.0010.001