Back to Multiple platform build/check report for BioC 3.13
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-20 15:05:36 -0400 (Mon, 20 Sep 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: 2021-09-19 04:50:10 -0400 (Sun, 19 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: /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: 2021-09-19 16:56:27 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 17:05:54 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 567.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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           34.515  1.132  44.476
scoreShift                 32.928  0.105  33.066
cumulativeCTSSdistribution 28.802  1.323  30.159
quantilePositions          28.664  0.380  29.059
aggregateTagClusters       16.725  0.087  16.823
clusterCTSS                 7.591  0.178   7.773
distclu-functions           7.066  0.182   7.253
CAGEexp-class               5.696  0.554   6.264
* 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

##############################################################################
##############################################################################
###
### 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-class5.6960.5546.264
CAGEr_Multicore0.8330.0150.849
CAGEset-class0.0020.0010.003
CTSS-class0.3450.0020.348
CTSSclusteringMethod0.0090.0000.009
CTSScoordinates0.1550.0020.157
CTSSnormalizedTpm1.2910.0201.312
CTSStagCount0.4640.0430.507
CTSStagCountTable0.0110.0010.011
CTSStoGenes0.9160.0030.918
CustomConsensusClusters1.7710.0061.777
GeneExpDESeq21.7720.0361.808
GeneExpSE0.0100.0010.010
QuantileWidthFunctions000
aggregateTagClusters16.725 0.08716.823
annotateCTSS2.9370.0112.952
byCtss0.0050.0000.006
clusterCTSS7.5910.1787.773
consensusClusterConvertors0.0390.0010.040
consensusClusters3.5350.2713.806
consensusClustersDESeq20.3880.0040.391
consensusClustersTpm0.0070.0010.007
coverage-functions4.2810.2834.566
cumulativeCTSSdistribution28.802 1.32330.159
distclu-functions7.0660.1827.253
exampleCAGEexp0.0000.0010.001
exampleCAGEset0.0130.0020.015
exportCTSStoBedGraph3.7580.0213.780
exportToBed3.5960.0213.623
expressionClasses0.0020.0010.003
extractExpressionClass0.0070.0010.008
genomeName000
getCTSS0.2100.0090.219
getExpressionProfiles0.6960.0020.699
getShiftingPromoters0.0040.0010.006
hanabi0.4250.0060.432
hanabiPlot0.6480.0110.660
import.CAGEscanMolecule0.0000.0010.000
import.CTSS0.1190.0030.121
import.bam0.0000.0010.000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData34.515 1.13244.476
inputFiles0.0000.0010.001
inputFilesType0.0010.0010.000
librarySizes0.0010.0010.000
mapStats0.0850.0060.090
mergeCAGEsets4.3870.0694.458
mergeSamples0.9720.0040.979
moleculesGR2CTSS0.2310.0010.233
normalizeTagCount1.1070.0541.161
parseCAGEscanBlocksToGrangeTSS0.0380.0010.039
plotAnnot2.7230.0272.754
plotCorrelation0.6580.0030.662
plotExpressionProfiles0.1630.0030.167
plotInterquantileWidth1.2490.0071.259
plotReverseCumulatives0.6450.0070.654
quantilePositions28.664 0.38029.059
ranges2annot0.4070.0020.408
ranges2genes0.0970.0020.098
ranges2names0.0910.0000.091
sampleLabels0.0010.0000.001
scoreShift32.928 0.10533.066
seqNameTotalsSE0.0090.0010.009
setColors2.2100.0082.219
strandInvaders1.4750.0661.549
summariseChrExpr0.9030.0130.915
tagClusterConvertors0.5860.0110.597
tagClusters0.1020.0040.106