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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2024-06-09 19:12:52 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 19:24:13 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 680.6 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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              32.828  0.319  33.204
aggregateTagClusters       31.387  1.283  32.769
clusterCTSS                30.709  0.256  31.018
scoreShift                 25.123  0.460  25.647
quantilePositions          23.610  0.691  24.357
annotateCTSS               23.119  0.722  23.890
cumulativeCTSSdistribution 21.426  1.212  22.697
CustomConsensusClusters    12.017  0.494  12.539
getExpressionProfiles      11.283  0.408  11.720
plotExpressionProfiles      9.783  0.288  10.090
CAGEexp-class               5.516  0.985   6.573
* 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-class5.5160.9856.573
CAGEr_Multicore3.5240.0113.539
CTSS-class0.3180.0030.321
CTSSclusteringMethod0.0010.0010.001
CTSScoordinates0.0980.0020.101
CTSSnormalizedTpm0.8780.0320.912
CTSStagCount0.9060.0830.993
CTSStoGenes0.4370.0160.453
CustomConsensusClusters12.017 0.49412.539
GeneExpDESeq20.4820.0170.502
GeneExpSE0.0030.0000.004
QuantileWidthFunctions0.1240.0010.124
aggregateTagClusters31.387 1.28332.769
annotateCTSS23.119 0.72223.890
byCtss0.0130.0000.013
clusterCTSS30.709 0.25631.018
consensusClusters0.1400.0030.143
consensusClustersDESeq23.5910.1733.769
consensusClustersTpm0.0040.0010.005
coverage-functions1.8400.0521.897
cumulativeCTSSdistribution21.426 1.21222.697
distclu-functions3.4830.3163.808
exampleCAGEexp0.0000.0010.001
exportToTrack32.828 0.31933.204
expressionClasses4.7740.0524.838
genomeName000
getCTSS1.1080.0171.127
getExpressionProfiles11.283 0.40811.720
getShiftingPromoters3.4270.1733.606
hanabi0.2750.0030.278
hanabiPlot0.3040.0060.312
import.CAGEscanMolecule000
import.CTSS0.0830.0020.085
import.bam0.0000.0010.000
import.bedCTSS0.0010.0000.000
import.bedScore000
import.bedmolecule0.0000.0000.001
inputFiles0.0010.0000.002
inputFilesType0.0010.0000.002
librarySizes0.0010.0000.001
mapStats0.0570.0050.062
mergeCAGEsets2.7780.0372.823
mergeSamples0.6140.0040.618
moleculesGR2CTSS0.1600.0010.161
normalizeTagCount0.5990.0070.608
parseCAGEscanBlocksToGrangeTSS0.0280.0010.029
plotAnnot2.4660.0252.500
plotCorrelation0.2160.0030.219
plotExpressionProfiles 9.783 0.28810.090
plotInterquantileWidth1.9770.0101.992
plotReverseCumulatives0.3410.0060.348
quantilePositions23.610 0.69124.357
quickEnhancers0.0010.0000.000
ranges2annot0.4690.0050.475
ranges2genes0.0600.0000.061
ranges2names0.0480.0000.048
resetCAGEexp0.3490.0010.351
rowSums.RleDataFrame0.0230.0000.023
rowsum.RleDataFrame0.0310.0000.031
sampleLabels0.0060.0000.006
scoreShift25.123 0.46025.647
seqNameTotalsSE0.0030.0000.003
setColors0.3860.0040.391
strandInvaders0.7880.0890.912
summariseChrExpr0.5160.0050.521
tagClusters0.2630.0070.270