Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:07:09 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 243/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.2.0  (landing page)
Charles Plessy
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_15
git_last_commit: 74d9a97
git_last_commit_date: 2022-04-26 11:13:41 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.2.0
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_2.2.0.tar.gz
StartedAt: 2022-06-24 00:19:35 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:33:48 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 853.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

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_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CAGEr.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.2.0’
* 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 ... OK
* 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
clusterCTSS                72.563  0.432  75.057
cumulativeCTSSdistribution 69.764  1.938  73.536
exportToTrack              63.410  0.129  64.181
quantilePositions          38.165  0.097  38.666
aggregateTagClusters       14.888  0.058  15.195
plotExpressionProfiles      9.162  0.213   9.520
CAGEexp-class               7.396  0.703   8.691
distclu-functions           6.631  0.338   7.164
coverage-functions          5.830  0.303   6.157
plotInterquantileWidth      5.781  0.031   5.853
mergeCAGEsets               5.121  0.026   5.190
* 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: OK


Installation output

CAGEr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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-class7.3960.7038.691
CAGEr_Multicore1.1670.0191.310
CTSS-class0.6500.0030.709
CTSSclusteringMethod0.0020.0000.002
CTSScoordinates0.1600.0020.182
CTSSnormalizedTpm1.5930.0421.843
CTSStagCount1.8250.1042.047
CTSStoGenes0.9010.0040.911
CustomConsensusClusters2.0450.0102.110
GeneExpDESeq22.4310.0412.514
GeneExpSE0.0090.0000.009
QuantileWidthFunctions0.2630.0020.270
aggregateTagClusters14.888 0.05815.195
annotateCTSS3.2000.0123.249
byCtss0.0090.0000.009
clusterCTSS72.563 0.43275.057
consensusClusters0.2790.0020.295
consensusClustersDESeq20.3870.0020.447
consensusClustersTpm0.0110.0000.012
coverage-functions5.8300.3036.157
cumulativeCTSSdistribution69.764 1.93873.536
distclu-functions6.6310.3387.164
exampleCAGEexp0.0000.0000.001
exportToTrack63.410 0.12964.181
expressionClasses0.0310.0010.033
genomeName0.0010.0000.000
getCTSS2.3540.0162.424
getExpressionProfiles4.7300.0134.771
getShiftingPromoters000
hanabi0.4420.0050.450
hanabiPlot0.5670.0230.592
import.CAGEscanMolecule0.0010.0000.000
import.CTSS0.1710.0020.173
import.bam0.0010.0000.000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule000
inputFiles0.0030.0010.002
inputFilesType0.0020.0000.002
librarySizes0.0020.0000.002
mapStats0.1180.0020.119
mergeCAGEsets5.1210.0265.190
mergeSamples1.2520.0041.263
moleculesGR2CTSS0.2710.0010.275
normalizeTagCount1.2090.0031.219
parseCAGEscanBlocksToGrangeTSS0.0480.0010.049
plotAnnot4.4300.0304.487
plotCorrelation0.5710.0040.580
plotExpressionProfiles9.1620.2139.520
plotInterquantileWidth5.7810.0315.853
plotReverseCumulatives0.6300.0040.644
quantilePositions38.165 0.09738.666
ranges2annot0.7770.0020.790
ranges2genes0.1260.0000.127
ranges2names0.1190.0010.120
sampleLabels0.0090.0010.009
scoreShift000
seqNameTotalsSE0.0080.0000.008
setColors0.9120.0050.920
strandInvaders1.4700.0921.583
summariseChrExpr1.1260.0031.141
tagClusters0.1900.0020.200