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This page was generated on 2024-03-28 11:38:53 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 262/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.9.0  (landing page)
Charles Plessy
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: 18d7295
git_last_commit_date: 2023-10-24 09:52:59 -0400 (Tue, 24 Oct 2023)
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  

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: 2.9.0
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_2.9.0.tar.gz
StartedAt: 2024-03-27 19:58:05 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:11:10 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 784.2 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_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘2.9.0’
* 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              40.594  0.615  41.538
aggregateTagClusters       37.899  1.570  39.821
clusterCTSS                38.122  0.538  39.020
scoreShift                 30.468  0.748  31.476
quantilePositions          28.030  1.030  29.293
annotateCTSS               26.582  0.915  27.731
cumulativeCTSSdistribution 25.427  1.548  27.241
CustomConsensusClusters    14.273  0.539  14.906
getExpressionProfiles      13.005  0.485  13.590
plotExpressionProfiles     10.537  0.309  10.930
CAGEexp-class               5.240  1.014   6.325
expressionClasses           5.567  0.083   5.686
* 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-class5.2401.0146.325
CAGEr_Multicore3.6760.0323.730
CTSS-class0.3300.0060.340
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0890.0020.091
CTSSnormalizedTpm0.8160.0220.843
CTSStagCount1.0640.1041.177
CTSStoGenes0.5300.0280.562
CustomConsensusClusters14.273 0.53914.906
GeneExpDESeq20.6450.0230.674
GeneExpSE0.0050.0000.006
QuantileWidthFunctions0.1780.0030.184
aggregateTagClusters37.899 1.57039.821
annotateCTSS26.582 0.91527.731
byCtss0.0190.0010.021
clusterCTSS38.122 0.53839.020
consensusClusters0.1410.0040.145
consensusClustersDESeq24.6710.1974.911
consensusClustersTpm0.0070.0010.008
coverage-functions2.0890.0752.181
cumulativeCTSSdistribution25.427 1.54827.241
distclu-functions4.0510.3634.449
exampleCAGEexp0.0000.0010.001
exportToTrack40.594 0.61541.538
expressionClasses5.5670.0835.686
genomeName0.0000.0000.001
getCTSS1.3570.0251.390
getExpressionProfiles13.005 0.48513.590
getShiftingPromoters4.3410.1724.541
hanabi0.2730.0030.277
hanabiPlot0.3470.0070.359
import.CAGEscanMolecule000
import.CTSS0.1040.0030.119
import.bam0.0000.0000.001
import.bedCTSS000
import.bedScore000
import.bedmolecule0.0000.0010.000
inputFiles0.0030.0010.003
inputFilesType0.0010.0010.002
librarySizes0.0010.0000.002
mapStats0.0650.0060.072
mergeCAGEsets3.0060.0563.088
mergeSamples0.7170.0080.730
moleculesGR2CTSS0.1740.0030.178
normalizeTagCount0.6960.0120.714
parseCAGEscanBlocksToGrangeTSS0.0270.0010.029
plotAnnot2.8870.0512.970
plotCorrelation0.3100.0050.319
plotExpressionProfiles10.537 0.30910.930
plotInterquantileWidth2.3310.0262.432
plotReverseCumulatives0.3850.0080.397
quantilePositions28.030 1.03029.293
quickEnhancers000
ranges2annot0.4110.0110.425
ranges2genes0.0980.0040.103
ranges2names0.0680.0010.070
resetCAGEexp0.3610.0040.369
rowSums.RleDataFrame0.0270.0010.028
rowsum.RleDataFrame0.0270.0010.027
sampleLabels0.0040.0010.005
scoreShift30.468 0.74831.476
seqNameTotalsSE0.0060.0000.006
setColors0.4880.0070.499
strandInvaders1.0510.1171.206
summariseChrExpr0.6650.0070.676
tagClusters0.2990.0070.312