Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-29 11:04:59 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4482
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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 CAGEr on nebbiolo2


To the developers/maintainers of the CAGEr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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 246/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.4.0  (landing page)
Charles Plessy
Snapshot Date: 2023-03-27 14:00:04 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_16
git_last_commit: 4ce371f
git_last_commit_date: 2022-11-01 11:07:54 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.4.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CAGEr_2.4.0.tar.gz
StartedAt: 2023-03-27 19:33:25 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 19:43:28 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 603.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CAGEr_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CAGEr.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.4.0’
* 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 ‘CAGEr’ 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 loading without being on the library search path ... 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
cumulativeCTSSdistribution 33.093  6.420  39.494
clusterCTSS                29.279  0.672  29.941
exportToTrack              25.881  0.092  25.972
quantilePositions          16.252  0.048  16.300
aggregateTagClusters        6.456  0.137   6.562
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CAGE_Resources.Rmd’ using ‘UTF-8’... OK
  ‘CAGEexp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘CAGEr’ ...
** 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class3.0180.1193.140
CAGEr_Multicore1.30.01.3
CTSS-class0.2730.0000.273
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0650.0040.070
CTSSnormalizedTpm0.6670.0600.727
CTSStagCount0.7950.0720.867
CTSStoGenes0.3420.0920.435
CustomConsensusClusters0.8580.0320.890
GeneExpDESeq21.0340.0241.058
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1230.0000.123
aggregateTagClusters6.4560.1376.562
annotateCTSS1.5590.0161.575
byCtss0.0020.0030.005
clusterCTSS29.279 0.67229.941
consensusClusters0.1130.0000.112
consensusClustersDESeq20.1570.0000.156
consensusClustersTpm0.0060.0000.005
coverage-functions3.8160.4684.284
cumulativeCTSSdistribution33.093 6.42039.494
distclu-functions3.6780.6364.266
exampleCAGEexp000
exportToTrack25.881 0.09225.972
expressionClasses0.0080.0040.012
genomeName000
getCTSS0.8880.0080.895
getExpressionProfiles1.5970.0121.609
getShiftingPromoters000
hanabi0.1960.0160.212
hanabiPlot0.3060.0080.314
import.CAGEscanMolecule000
import.CTSS0.0700.0040.073
import.bam0.0000.0000.001
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0000.0010.002
inputFilesType0.0000.0010.001
librarySizes0.0010.0010.001
mapStats0.0490.0000.049
mergeCAGEsets2.0110.0002.011
mergeSamples0.4580.0000.457
moleculesGR2CTSS0.1290.0000.129
normalizeTagCount0.4780.0080.465
parseCAGEscanBlocksToGrangeTSS0.0210.0000.021
plotAnnot2.4850.0602.545
plotCorrelation0.2360.0040.240
plotExpressionProfiles4.4290.0324.461
plotInterquantileWidth1.9650.0001.965
plotReverseCumulatives0.3840.0000.332
quantilePositions16.252 0.04816.300
ranges2annot0.3490.0040.353
ranges2genes0.0550.0000.055
ranges2names0.0530.0000.053
sampleLabels0.0050.0000.004
scoreShift0.0000.0000.001
seqNameTotalsSE0.0040.0000.004
setColors0.5050.0000.505
strandInvaders0.6510.0240.647
summariseChrExpr0.4610.0000.461
tagClusters0.0830.0000.084