Back to Multiple platform build/check report for BioC 3.13
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-20 15:05:36 -0400 (Mon, 20 Sep 2021).

CHECK results for CAGEfightR on machv2

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 230/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.12.0  (landing page)
Malte Thodberg
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_13
git_last_commit: f776ea4
git_last_commit_date: 2021-05-19 12:35:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEfightR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz
StartedAt: 2021-09-19 16:56:18 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 17:03:38 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 439.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... 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         5.817  1.545   5.781
calcShape         5.207  0.185   5.395
assignGeneID      4.991  0.132   5.165
trimToPercentiles 5.066  0.032   5.101
* 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-3.13-bioc/meat/CAGEfightR.Rcheck/00check.log’
for details.



Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
assignGeneID4.9910.1325.165
assignMissingID1.8600.0401.899
assignTxID1.4420.0311.472
assignTxType0.0000.0000.001
balanceBC0.0000.0000.001
balanceD0.0010.0000.001
bwCommonGenome0.0470.0060.053
bwGenomeCompatibility0.0180.0040.021
bwValid0.0110.0040.014
calcBidirectionality0.7390.0170.756
calcComposition3.1500.0633.214
calcPooled0.2840.0040.288
calcShape5.2070.1855.395
calcSupport0.2360.0030.239
calcTPM0.2840.0080.292
calcTotalTags0.1190.0040.122
checkCTSSs0.4660.0050.472
checkPeaked0.2280.0350.263
checkPooled0.0810.0030.083
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally2.5700.0332.605
combineClusters1.8090.0311.844
convertBAM2BigWig0.0000.0000.001
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.1650.0110.176
exampleDesign0.0070.0110.019
findLinks5.8171.5455.781
findStretches0.8700.0820.952
quantifyCTSSs0.0010.0010.001
quantifyCTSSs20.0000.0010.001
quantifyClusters0.9740.0901.064
quantifyGenes2.0370.1112.149
quickEnhancers0.0010.0000.000
quickGenes0.0000.0000.001
quickTSSs000
shapeEntropy0.0010.0010.001
shapeIQR0.0010.0010.001
shapeMean0.0010.0010.001
shapeMultimodality000
subsetByBidirectionality0.7000.0210.722
subsetByComposition2.1010.0442.147
subsetBySupport0.1830.0030.187
swapRanges0.3370.0060.342
swapScores0.2860.0220.308
trackBalance0.0000.0010.001
trackCTSS4.2520.2374.497
trackClusters2.9390.0322.971
trackLinks1.9090.8751.934
trimToPeak2.0760.1672.245
trimToPercentiles5.0660.0325.101
tuneTagClustering0.0000.0010.001
utilsAggregateRows0.6660.5601.263
utilsDeStrand0.1980.0040.202
utilsScoreOverlaps0.1050.0000.106
utilsSimplifyTxDb0.0010.0000.000