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This page was generated on 2022-01-22 11:09:53 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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? here 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 232/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.15.1  (landing page)
Malte Thodberg
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: master
git_last_commit: aead2e0
git_last_commit_date: 2021-11-20 23:19:47 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEfightR
Version: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2022-01-21 22:50:19 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 22:59:25 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 546.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CAGEfightR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.15.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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    5.799  1.700   5.783
assignGeneID 5.731  0.136   5.915
trackCTSS    5.515  0.252   5.878
calcShape    5.427  0.270   5.711
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/CAGEfightR.Rcheck/00check.log’
for details.



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
assignGeneID5.7310.1365.915
assignMissingID2.7760.0322.813
assignTxID1.5220.0301.557
assignTxType0.0000.0010.001
balanceBC0.0010.0000.001
balanceD0.0010.0000.001
bwCommonGenome0.0640.0060.072
bwGenomeCompatibility0.0340.0040.038
bwValid0.0140.0040.018
calcBidirectionality0.7970.0270.826
calcComposition2.3680.0522.421
calcPooled0.1680.0050.173
calcShape5.4270.2705.711
calcSupport0.1900.0060.196
calcTPM0.1980.0030.201
calcTotalTags0.1140.0050.120
checkCTSSs0.4930.0070.502
checkPeaked0.1630.0100.174
checkPooled0.0990.0050.104
clusterBidirectionally000
clusterUnidirectionally2.4430.0152.459
combineClusters1.4440.0361.482
convertBAM2BigWig000
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.1320.0000.133
exampleDesign0.0080.0110.020
findLinks5.7991.7005.783
findStretches0.6570.0760.735
quantifyCTSSs0.0010.0010.001
quantifyCTSSs20.0000.0010.000
quantifyClusters0.7370.0680.805
quantifyGenes2.3820.1382.627
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0010.001
shapeMean0.0000.0000.001
shapeMultimodality0.0010.0000.000
subsetByBidirectionality0.8770.0630.946
subsetByComposition2.4210.0372.568
subsetBySupport0.1560.0090.171
swapRanges0.3930.0180.429
swapScores0.2170.0050.230
trackBalance0.0000.0010.000
trackCTSS5.5150.2525.878
trackClusters3.0560.0303.090
trackLinks2.0111.1152.053
trimToPeak1.4370.1251.563
trimToPercentiles3.7430.1043.851
tuneTagClustering0.0000.0000.001
utilsAggregateRows0.6950.3161.012
utilsDeStrand0.2100.0030.214
utilsScoreOverlaps0.1200.0000.121
utilsSimplifyTxDb0.0010.0000.001