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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).

CHECK results for CAGEr on machv2

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 231/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.34.0  (landing page)
Charles Plessy
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.34.0.tar.gz
StartedAt: 2021-10-14 17:01:21 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:10:51 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 570.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.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 ‘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 ... 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 ‘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
importPublicData           34.819  1.138  45.438
scoreShift                 32.768  0.091  32.887
quantilePositions          31.197  0.420  31.638
cumulativeCTSSdistribution 29.098  1.329  30.444
aggregateTagClusters       15.950  0.102  16.081
distclu-functions           7.552  0.198   7.758
clusterCTSS                 6.822  0.157   6.982
CAGEexp-class               5.742  0.616   6.388
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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


* 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-class5.7420.6166.388
CAGEr_Multicore0.9170.0230.945
CAGEset-class0.0020.0010.003
CTSS-class0.5490.0050.558
CTSSclusteringMethod0.0110.0000.011
CTSScoordinates0.1850.0020.188
CTSSnormalizedTpm1.3440.0291.378
CTSStagCount0.410.040.45
CTSStagCountTable0.0080.0010.010
CTSStoGenes1.1150.0071.127
CustomConsensusClusters1.8980.0101.911
GeneExpDESeq21.7740.0431.824
GeneExpSE0.0100.0010.011
QuantileWidthFunctions0.0000.0010.000
aggregateTagClusters15.950 0.10216.081
annotateCTSS2.5540.0122.569
byCtss0.0070.0010.008
clusterCTSS6.8220.1576.982
consensusClusterConvertors0.0510.0030.053
consensusClusters3.5090.2273.738
consensusClustersDESeq20.4160.0040.421
consensusClustersTpm0.0090.0000.010
coverage-functions4.5380.3104.852
cumulativeCTSSdistribution29.098 1.32930.444
distclu-functions7.5520.1987.758
exampleCAGEexp0.0010.0010.001
exampleCAGEset0.0130.0010.014
exportCTSStoBedGraph4.5830.0264.652
exportToBed4.1610.0144.177
expressionClasses0.0030.0010.003
extractExpressionClass0.0070.0010.009
genomeName0.0000.0000.001
getCTSS0.2170.0110.228
getExpressionProfiles0.6790.0020.682
getShiftingPromoters0.0090.0030.011
hanabi0.3960.0040.400
hanabiPlot0.6400.0170.659
import.CAGEscanMolecule000
import.CTSS0.1110.0010.112
import.bam0.0000.0010.000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData34.819 1.13845.438
inputFiles0.0000.0010.001
inputFilesType0.0000.0010.001
librarySizes0.0010.0010.001
mapStats0.0670.0050.073
mergeCAGEsets4.1410.0424.186
mergeSamples1.4280.0041.432
moleculesGR2CTSS0.2310.0010.232
normalizeTagCount1.0580.0471.105
parseCAGEscanBlocksToGrangeTSS0.0450.0010.047
plotAnnot3.0590.0303.098
plotCorrelation0.6270.0030.630
plotExpressionProfiles0.1550.0040.160
plotInterquantileWidth1.4260.0111.442
plotReverseCumulatives0.8490.0070.859
quantilePositions31.197 0.42031.638
ranges2annot0.4110.0020.413
ranges2genes0.1050.0010.107
ranges2names0.0730.0010.073
sampleLabels0.0000.0000.001
scoreShift32.768 0.09132.887
seqNameTotalsSE0.0080.0010.009
setColors1.9400.0111.954
strandInvaders1.3380.0561.405
summariseChrExpr0.9480.0050.953
tagClusterConvertors0.4970.0070.505
tagClusters0.1010.0040.105