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This page was generated on 2024-05-04 11:38:56 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 264/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.10.0  (landing page)
Charles Plessy
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_19
git_last_commit: 6c8b145
git_last_commit_date: 2024-04-30 10:30:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for CAGEr on lconway


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: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2024-05-03 20:37:41 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:50:16 -0400 (Fri, 03 May 2024)
EllapsedTime: 755.3 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_2.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.10.0’
* 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 ... NOTE
checkRd: (-1) inputFiles.Rd:28: Lost braces
    28 | code{\link{CAGEexp}} objects.
       |     ^
checkRd: (-1) inputFilesType.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:53-55: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
S3 methods shown with full name in Rd file 'rowsum.RleDataFrame.Rd':
  'rowsum.RleDataFrame'

The \usage entries for S3 methods should use the \method markup and not
their full name.
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
exportToTrack              39.181  0.613  40.106
aggregateTagClusters       36.079  1.529  37.903
clusterCTSS                35.849  0.593  36.780
scoreShift                 28.305  0.750  29.359
quantilePositions          26.329  1.007  27.625
annotateCTSS               26.243  0.927  27.393
cumulativeCTSSdistribution 25.283  1.567  27.107
CustomConsensusClusters    13.012  0.550  13.689
getExpressionProfiles      12.502  0.492  13.094
plotExpressionProfiles     11.473  0.365  11.927
CAGEexp-class               5.230  1.049   6.368
expressionClasses           5.523  0.088   5.652
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


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/4.4-x86_64/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-class5.2301.0496.368
CAGEr_Multicore3.7050.0333.762
CTSS-class0.3460.0050.352
CTSSclusteringMethod0.0020.0000.001
CTSScoordinates0.0950.0030.098
CTSSnormalizedTpm0.8190.0340.858
CTSStagCount1.0890.1071.206
CTSStoGenes0.5750.0300.614
CustomConsensusClusters13.012 0.55013.689
GeneExpDESeq20.5880.0240.618
GeneExpSE0.0050.0000.005
QuantileWidthFunctions0.1550.0020.158
aggregateTagClusters36.079 1.52937.903
annotateCTSS26.243 0.92727.393
byCtss0.0200.0010.021
clusterCTSS35.849 0.59336.780
consensusClusters0.1850.0110.199
consensusClustersDESeq24.6790.2194.946
consensusClustersTpm0.0070.0010.008
coverage-functions2.2240.0732.321
cumulativeCTSSdistribution25.283 1.56727.107
distclu-functions4.0470.3714.506
exampleCAGEexp0.0000.0010.001
exportToTrack39.181 0.61340.106
expressionClasses5.5230.0885.652
genomeName0.0000.0000.001
getCTSS1.3040.0251.338
getExpressionProfiles12.502 0.49213.094
getShiftingPromoters4.0490.1774.249
hanabi0.2630.0040.268
hanabiPlot0.3250.0070.335
import.CAGEscanMolecule0.0000.0000.001
import.CTSS0.1060.0030.110
import.bam0.0000.0000.001
import.bedCTSS000
import.bedScore0.0000.0000.001
import.bedmolecule000
inputFiles0.0030.0010.003
inputFilesType0.0020.0010.003
librarySizes0.0010.0000.001
mapStats0.0530.0040.059
mergeCAGEsets2.6490.0432.704
mergeSamples0.6800.0100.695
moleculesGR2CTSS0.1630.0020.165
normalizeTagCount0.6140.0090.627
parseCAGEscanBlocksToGrangeTSS0.0240.0000.024
plotAnnot2.7310.0452.802
plotCorrelation0.2930.0060.303
plotExpressionProfiles11.473 0.36511.927
plotInterquantileWidth2.2950.0252.338
plotReverseCumulatives0.4260.0100.441
quantilePositions26.329 1.00727.625
quickEnhancers000
ranges2annot0.4600.0070.470
ranges2genes0.0710.0010.073
ranges2names0.0740.0010.077
resetCAGEexp0.3630.0050.373
rowSums.RleDataFrame0.0180.0000.018
rowsum.RleDataFrame0.0240.0010.025
sampleLabels0.0060.0010.006
scoreShift28.305 0.75029.359
seqNameTotalsSE0.0050.0000.006
setColors0.5170.0100.533
strandInvaders1.0500.1041.182
summariseChrExpr0.5990.0090.613
tagClusters0.3250.0100.338