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This page was generated on 2021-09-22 15:04:47 -0400 (Wed, 22 Sep 2021).

CHECK results for CAGEr on nebbiolo1

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.
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raw results

Package 231/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.34.0  (landing page)
Charles Plessy
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_13
git_last_commit: 8e7ccda
git_last_commit_date: 2021-05-19 11:57:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 1.34.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAGEr_1.34.0.tar.gz
StartedAt: 2021-09-21 09:07:20 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:16:50 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 569.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAGEr_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.34.0’
* 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 ... WARNING
Missing link or links in documentation object 'CustomConsensusClusters.Rd':
  ‘.ConsensusClusters’

Missing link or links in documentation object 'clusterCTSS.Rd':
  ‘TagClusters’

Missing link or links in documentation object 'consensusClusters.Rd':
  ‘ConsensusClusters’

Missing link or links in documentation object 'tagClusters.Rd':
  ‘TagClusters’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'CTSS'
All user-level objects in a package (including S4 classes and methods)
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 ... WARNING
Undocumented arguments in documentation object 'CTSS-class'
  ‘.Object’ ‘...’ ‘bsgenomeName’ ‘seqnames’ ‘pos’ ‘strand’ ‘seqinfo’
  ‘seqlengths’ ‘from’ ‘to’ ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
scoreShift                 40.393  0.281  40.675
importPublicData           30.319  1.937  77.626
cumulativeCTSSdistribution 24.413  5.887  30.284
quantilePositions          19.220  0.416  19.636
aggregateTagClusters       10.286  0.032  10.286
clusterCTSS                 6.802  0.476   7.238
distclu-functions           6.201  0.808   6.945
* 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: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-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-class4.1830.6924.891
CAGEr_Multicore0.9410.0040.943
CAGEset-class0.0030.0000.003
CTSS-class0.2740.0070.282
CTSSclusteringMethod0.0090.0000.009
CTSScoordinates0.0970.0000.096
CTSSnormalizedTpm0.8590.0120.822
CTSStagCount0.2980.0270.326
CTSStagCountTable0.0060.0000.006
CTSStoGenes0.6480.0040.652
CustomConsensusClusters1.4410.0041.445
GeneExpDESeq21.2280.0201.248
GeneExpSE0.0040.0020.006
QuantileWidthFunctions000
aggregateTagClusters10.286 0.03210.286
annotateCTSS1.7120.0161.727
byCtss0.0050.0000.006
clusterCTSS6.8020.4767.238
consensusClusterConvertors0.0290.0000.029
consensusClusters2.5750.4723.046
consensusClustersDESeq20.2870.0000.286
consensusClustersTpm0.0060.0000.007
coverage-functions3.5570.5684.125
cumulativeCTSSdistribution24.413 5.88730.284
distclu-functions6.2010.8086.945
exampleCAGEexp0.0010.0000.000
exampleCAGEset0.0100.0040.013
exportCTSStoBedGraph2.6880.0162.703
exportToBed1.9660.0211.986
expressionClasses0.0020.0000.003
extractExpressionClass0.0110.0000.011
genomeName0.0010.0000.000
getCTSS0.2090.0160.189
getExpressionProfiles0.1360.0040.140
getShiftingPromoters0.0050.0000.005
hanabi0.3060.0040.310
hanabiPlot0.5370.0040.540
import.CAGEscanMolecule000
import.CTSS0.0810.0040.085
import.bam000
import.bedCTSS000
import.bedScore0.0010.0000.000
import.bedmolecule0.0000.0000.001
importPublicData30.319 1.93777.626
inputFiles0.0000.0000.001
inputFilesType0.0000.0010.001
librarySizes000
mapStats0.0420.0060.048
mergeCAGEsets2.7130.0642.751
mergeSamples0.7840.0130.797
moleculesGR2CTSS0.1370.0120.149
normalizeTagCount1.9580.1282.051
parseCAGEscanBlocksToGrangeTSS0.0260.0000.026
plotAnnot1.7990.0481.847
plotCorrelation0.4480.0040.452
plotExpressionProfiles0.1340.0000.135
plotInterquantileWidth0.8040.0160.819
plotReverseCumulatives0.6290.0120.548
quantilePositions19.220 0.41619.636
ranges2annot0.3580.0040.363
ranges2genes0.0680.0000.068
ranges2names0.0660.0000.066
sampleLabels0.0010.0000.000
scoreShift40.393 0.28140.675
seqNameTotalsSE0.0000.0060.006
setColors1.3520.0371.389
strandInvaders1.0220.1471.160
summariseChrExpr0.6570.0010.658
tagClusterConvertors0.3250.0110.336
tagClusters0.0620.0010.062