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This page was generated on 2021-10-26 14:06:18 -0400 (Tue, 26 Oct 2021).

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? 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: 2021-10-25 14:50:11 -0400 (Mon, 25 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
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  

Summary

Package: CAGEr
Version: 1.99.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEr_1.99.0.tar.gz
StartedAt: 2021-10-25 19:23:52 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 19:30:14 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 381.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEr_1.99.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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
cumulativeCTSSdistribution 23.230  7.076  30.289
exportToTrack              27.678  0.144  27.823
quantilePositions          17.414  0.152  17.566
aggregateTagClusters        8.592  0.145   8.689
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-class4.0050.2164.224
CAGEr_Multicore0.9280.0090.934
CTSS-class0.3240.0000.324
CTSSclusteringMethod0.0000.0000.001
CTSScoordinates0.0770.0000.077
CTSSnormalizedTpm0.7370.0110.749
CTSStagCount0.8970.0370.933
CTSStoGenes0.5030.0000.503
CustomConsensusClusters1.1300.0111.142
GeneExpDESeq21.1740.0281.202
GeneExpSE0.0110.0000.011
QuantileWidthFunctions000
aggregateTagClusters8.5920.1458.689
annotateCTSS1.7300.0081.738
byCtss0.0050.0000.005
clusterCTSS3.8820.4844.343
consensusClusters0.1720.0040.176
consensusClustersDESeq20.3070.0000.307
consensusClustersTpm0.0080.0000.008
coverage-functions2.980.463.44
cumulativeCTSSdistribution23.230 7.07630.289
distclu-functions3.8290.7164.478
exampleCAGEexp0.0000.0000.001
exportToTrack27.678 0.14427.823
expressionClasses0.0160.0000.017
genomeName000
getCTSS1.1740.0161.189
getExpressionProfiles1.9480.0121.960
getShiftingPromoters000
hanabi0.2210.0240.245
hanabiPlot0.2770.0000.277
import.CAGEscanMolecule000
import.CTSS0.0820.0000.081
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0000.0010.000
inputFilesType0.0000.0010.001
librarySizes0.0000.0000.001
mapStats0.0300.0040.034
mergeCAGEsets2.4700.0362.506
mergeSamples0.5890.0080.597
moleculesGR2CTSS0.1450.0080.153
normalizeTagCount0.7550.0200.753
parseCAGEscanBlocksToGrangeTSS0.0310.0000.031
plotAnnot1.7050.0241.729
plotCorrelation0.4120.0000.412
plotExpressionProfiles3.7090.0913.800
plotInterquantileWidth2.6100.0042.614
plotReverseCumulatives0.4920.0040.439
quantilePositions17.414 0.15217.566
ranges2annot0.3930.0000.393
ranges2genes0.0510.0000.052
ranges2names0.0510.0000.051
sampleLabels0.0010.0000.002
scoreShift000
seqNameTotalsSE0.0110.0000.011
setColors0.5210.0070.529
strandInvaders0.8060.0440.837
summariseChrExpr0.7160.0160.732
tagClusters0.1310.0000.130