Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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 nebbiolo1


To the developers/maintainers of the CAGEr package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 258/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.5.0  (landing page)
Charles Plessy
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: 3cc0923
git_last_commit_date: 2022-11-01 11:07:54 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: CAGEr
Version: 2.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CAGEr_2.5.0.tar.gz
StartedAt: 2023-04-11 19:03:02 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 19:13:10 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 607.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CAGEr_2.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEr.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.5.0’
* 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 loading without being on the library search path ... 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
cumulativeCTSSdistribution 33.085  6.983  40.054
clusterCTSS                30.152  0.920  31.062
exportToTrack              27.514  0.140  27.654
quantilePositions          16.575  0.024  16.600
aggregateTagClusters        6.321  0.144   6.439
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CAGE_Resources.Rmd’ using ‘UTF-8’... OK
  ‘CAGEexp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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-class1.6440.0801.728
CAGEr_Multicore2.8940.1283.023
CTSS-class0.2660.0000.266
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0660.0000.067
CTSSnormalizedTpm0.6600.0720.732
CTSStagCount0.7640.0680.832
CTSStoGenes0.3150.0080.323
CustomConsensusClusters0.8390.0120.850
GeneExpDESeq20.4060.0080.413
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1000.0040.104
aggregateTagClusters6.3210.1446.439
annotateCTSS1.4130.0241.437
byCtss0.0060.0000.007
clusterCTSS30.152 0.92031.062
consensusClusters0.1190.0000.120
consensusClustersDESeq20.1690.0000.169
consensusClustersTpm0.0030.0040.006
coverage-functions3.4320.4283.860
cumulativeCTSSdistribution33.085 6.98340.054
distclu-functions3.5170.7214.189
exampleCAGEexp0.0000.0000.001
exportToTrack27.514 0.14027.654
expressionClasses0.0110.0040.014
genomeName0.0010.0000.000
getCTSS0.8540.0240.877
getExpressionProfiles1.4120.0031.417
getShiftingPromoters0.0000.0000.001
hanabi0.2260.0280.253
hanabiPlot0.2640.0120.276
import.CAGEscanMolecule000
import.CTSS0.0730.0040.078
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0020.0000.001
inputFilesType0.0000.0010.001
librarySizes0.0000.0010.001
mapStats0.0440.0050.048
mergeCAGEsets1.9680.0432.012
mergeSamples0.4320.0000.433
moleculesGR2CTSS0.1460.0080.154
normalizeTagCount0.4800.0030.462
parseCAGEscanBlocksToGrangeTSS0.0250.0000.025
plotAnnot2.7350.0202.755
plotCorrelation0.2590.0000.259
plotExpressionProfiles4.7790.0954.876
plotInterquantileWidth2.0500.0152.066
plotReverseCumulatives0.3290.0040.291
quantilePositions16.575 0.02416.600
ranges2annot0.3910.0080.398
ranges2genes0.0580.0000.058
ranges2names0.0580.0000.059
sampleLabels0.0050.0000.005
scoreShift0.0010.0000.000
seqNameTotalsSE0.0040.0000.004
setColors0.3040.0020.306
strandInvaders0.5740.0820.643
summariseChrExpr0.3530.0040.357
tagClusters0.0850.0000.085