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This page was generated on 2024-03-01 11:37:33 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 261/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.8.0  (landing page)
Charles Plessy
Snapshot Date: 2024-02-29 14:05:06 -0500 (Thu, 29 Feb 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_18
git_last_commit: 6ad953b
git_last_commit_date: 2023-10-24 09:52:59 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 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: 2.8.0
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_2.8.0.tar.gz
StartedAt: 2024-02-29 19:20:05 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 19:32:18 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 733.4 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_2.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/CAGEr.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘2.8.0’
* 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 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 ... NOTE
S3 methods shown with full name in documentation object 'rowsum.RleDataFrame':
  '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
aggregateTagClusters       35.058  1.449  36.738
exportToTrack              34.896  0.497  35.564
clusterCTSS                34.270  0.528  35.027
quantilePositions          26.166  0.944  27.288
scoreShift                 26.133  0.733  27.018
annotateCTSS               24.323  0.837  25.340
cumulativeCTSSdistribution 22.794  1.397  24.318
CustomConsensusClusters    13.019  0.600  13.711
getExpressionProfiles      13.045  0.300  13.426
plotExpressionProfiles      9.396  0.362   9.833
CAGEexp-class               5.229  1.042   6.332
getShiftingPromoters        5.296  0.281   5.621
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-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-class5.2291.0426.332
CAGEr_Multicore3.5640.0363.616
CTSS-class0.3110.0030.317
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0860.0030.089
CTSSnormalizedTpm0.8510.0150.873
CTSStagCount1.0250.0821.119
CTSStoGenes0.5020.0320.538
CustomConsensusClusters13.019 0.60013.711
GeneExpDESeq20.5910.0200.616
GeneExpSE0.0050.0000.006
QuantileWidthFunctions0.1790.0020.204
aggregateTagClusters35.058 1.44936.738
annotateCTSS24.323 0.83725.340
byCtss0.0220.0010.023
clusterCTSS34.270 0.52835.027
consensusClusters0.1170.0050.123
consensusClustersDESeq24.0810.1924.303
consensusClustersTpm0.0050.0010.006
coverage-functions1.9560.0622.033
cumulativeCTSSdistribution22.794 1.39724.318
distclu-functions3.7780.3474.157
exampleCAGEexp000
exportToTrack34.896 0.49735.564
expressionClasses3.9230.1484.092
genomeName0.0000.0010.001
getCTSS1.3140.0211.340
getExpressionProfiles13.045 0.30013.426
getShiftingPromoters5.2960.2815.621
hanabi0.2780.0060.286
hanabiPlot0.3420.0120.357
import.CAGEscanMolecule000
import.CTSS0.0890.0020.092
import.bam0.0000.0010.000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0020.0000.002
inputFilesType0.0010.0010.001
librarySizes0.0010.0000.002
mapStats0.0650.0070.074
mergeCAGEsets2.7120.0422.769
mergeSamples0.6600.0080.673
moleculesGR2CTSS0.1650.0020.167
normalizeTagCount0.6660.0120.685
parseCAGEscanBlocksToGrangeTSS0.0310.0010.033
plotAnnot2.4460.0332.492
plotCorrelation0.2550.0040.260
plotExpressionProfiles9.3960.3629.833
plotInterquantileWidth2.1020.0182.128
plotReverseCumulatives0.3770.0090.390
quantilePositions26.166 0.94427.288
quickEnhancers000
ranges2annot0.4080.0040.420
ranges2genes0.0700.0010.070
ranges2names0.0720.0000.073
resetCAGEexp0.3770.0040.384
rowSums.RleDataFrame0.0290.0010.030
rowsum.RleDataFrame0.0280.0010.029
sampleLabels0.0060.0010.007
scoreShift26.133 0.73327.018
seqNameTotalsSE0.0040.0000.005
setColors0.4780.0070.489
strandInvaders0.9230.0941.041
summariseChrExpr0.5750.0460.648
tagClusters0.1870.0030.190