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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 266/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.12.0  (landing page)
Charles Plessy
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_20
git_last_commit: 492797d
git_last_commit_date: 2024-10-29 09:44:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CAGEr on kjohnson1

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CAGEr
Version: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2024-12-20 13:28:31 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 13:39:30 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 659.2 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_2.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.12.0’
* 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 code 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
paraclu                41.285  0.125  41.423
exportToTrack          34.463  0.166  34.690
aggregateTagClusters   20.240  0.164  20.442
scoreShift             18.817  0.160  18.987
quantilePositions      13.128  0.072  13.203
annotateCTSS           12.167  0.051  12.219
distclu                 9.384  0.042   9.429
plotExpressionProfiles  7.459  0.165   7.625
CAGEexp-class           5.644  0.646   6.308
getExpressionProfiles   5.423  0.026   5.452
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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-class5.6440.6466.308
CAGEr_Multicore4.8910.0334.924
CTSS-class0.2650.0070.272
CTSScoordinates0.0870.0030.090
CTSSnormalizedTpm0.7190.0170.736
CTSStagCount0.6990.0580.756
CTSStoGenes0.5160.0230.539
CustomConsensusClusters4.7070.0364.744
GeneExpDESeq20.5420.0110.553
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1640.0030.167
TSSlogo2.5760.0442.627
aggregateTagClusters20.240 0.16420.442
annotateCTSS12.167 0.05112.219
byCtss0.0220.0000.022
consensusClusters0.1540.0020.157
consensusClustersDESeq21.8980.0071.925
consensusClustersTpm0.0060.0000.007
cumulativeCTSSdistribution4.260.074.35
distclu9.3840.0429.429
dot-ctss_summary_for_clusters0.8750.0060.882
exampleCAGEexp0.0000.0000.001
exportToTrack34.463 0.16634.690
expressionClasses1.7650.0051.769
filteredCTSSidx0.0130.0000.013
flagLowExpCTSS0.0400.0000.039
genomeName0.0010.0000.000
getCTSS1.1480.0191.166
getExpressionProfiles5.4230.0265.452
getShiftingPromoters1.7970.0051.803
hanabi0.2610.0060.267
hanabiPlot0.3020.0100.314
import.CAGEscanMolecule000
import.CTSS0.1190.0050.123
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0010.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0010.002
librarySizes0.0020.0000.002
mapStats0.0570.0030.060
mergeCAGEsets2.4590.0382.508
mergeSamples0.6140.0050.619
moleculesGR2CTSS0.1290.0010.130
normalizeTagCount0.8590.0360.681
paraclu41.285 0.12541.423
parseCAGEscanBlocksToGrangeTSS0.0260.0010.028
plotAnnot2.3760.0602.440
plotCorrelation0.2570.0050.263
plotExpressionProfiles7.4590.1657.625
plotInterquantileWidth2.1500.0112.163
plotReverseCumulatives2.8710.2062.435
quantilePositions13.128 0.07213.203
quickEnhancers000
ranges2annot0.3680.0020.370
ranges2genes0.0620.0010.064
ranges2names0.0590.0010.060
resetCAGEexp0.3730.0030.377
rowSums.RleDataFrame0.0220.0010.023
rowsum.RleDataFrame0.0250.0010.026
sampleLabels0.0040.0000.005
scoreShift18.817 0.16018.987
seqNameTotalsSE0.0030.0000.004
setColors0.4340.0040.438
strandInvaders0.8020.0840.887
summariseChrExpr0.5850.0170.603
tagClusters0.4360.0140.450