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This page was generated on 2021-10-23 14:06:54 -0400 (Sat, 23 Oct 2021).

CHECK results for CAGEr on merida1

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? 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 237/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.99.0  (landing page)
Charles Plessy
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: master
git_last_commit: d4049ac
git_last_commit_date: 2021-07-04 20:39:25 -0400 (Sun, 04 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 1.99.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_1.99.0.tar.gz
StartedAt: 2021-10-23 01:32:02 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 01:41:25 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 563.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_1.99.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.99.0’
* 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 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 ... WARNING
Undocumented code objects:
  ‘FANTOM5humanSamples’ ‘FANTOM5mouseSamples’
Undocumented data sets:
  ‘FANTOM5humanSamples’ ‘FANTOM5mouseSamples’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
exportToTrack              51.264  0.138  51.467
cumulativeCTSSdistribution 31.566  1.653  33.252
quantilePositions          27.875  0.306  28.209
aggregateTagClusters       13.736  0.094  13.878
plotExpressionProfiles      6.613  0.138   6.762
CAGEexp-class               5.969  0.594   6.581
distclu-functions           5.502  0.279   5.786
clusterCTSS                 5.176  0.153   5.350
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-class5.9690.5946.581
CAGEr_Multicore0.9480.0250.979
CTSS-class0.6140.0020.618
CTSSclusteringMethod0.0010.0000.002
CTSScoordinates0.1390.0020.141
CTSSnormalizedTpm1.3100.0541.373
CTSStagCount1.3530.0291.386
CTSStoGenes0.6370.0020.639
CustomConsensusClusters1.7860.0071.795
GeneExpDESeq21.9700.0332.005
GeneExpSE0.0140.0000.014
QuantileWidthFunctions000
aggregateTagClusters13.736 0.09413.878
annotateCTSS2.8750.0192.905
byCtss0.0050.0000.005
clusterCTSS5.1760.1535.350
consensusClusters0.3000.0010.301
consensusClustersDESeq20.6220.0030.627
consensusClustersTpm0.0130.0000.013
coverage-functions3.0830.2633.358
cumulativeCTSSdistribution31.566 1.65333.252
distclu-functions5.5020.2795.786
exampleCAGEexp0.0000.0000.001
exportToTrack51.264 0.13851.467
expressionClasses0.0220.0000.023
genomeName0.0010.0000.001
getCTSS1.7930.0121.807
getExpressionProfiles3.8920.0103.908
getShiftingPromoters000
hanabi0.3740.0050.379
hanabiPlot0.4580.0110.471
import.CAGEscanMolecule000
import.CTSS0.1470.0020.148
import.bam000
import.bedCTSS0.0000.0010.001
import.bedScore000
import.bedmolecule000
inputFiles0.0000.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.001
mapStats0.0580.0020.059
mergeCAGEsets4.2060.0234.233
mergeSamples0.8830.0030.886
moleculesGR2CTSS0.2120.0010.214
normalizeTagCount1.1260.0041.131
parseCAGEscanBlocksToGrangeTSS0.0430.0010.044
plotAnnot2.8530.0222.883
plotCorrelation0.7180.0050.726
plotExpressionProfiles6.6130.1386.762
plotInterquantileWidth4.5670.0134.587
plotReverseCumulatives0.6220.0030.627
quantilePositions27.875 0.30628.209
ranges2annot0.7570.0020.760
ranges2genes0.1220.0010.123
ranges2names0.1170.0010.118
sampleLabels0.0020.0000.003
scoreShift000
seqNameTotalsSE0.0470.0000.048
setColors0.8910.0030.895
strandInvaders1.3910.1821.586
summariseChrExpr0.9950.0031.000
tagClusters0.2150.0010.216