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This page was generated on 2024-03-02 11:35:36 -0500 (Sat, 02 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: 2024-03-01 14:05:09 -0500 (Fri, 01 Mar 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 nebbiolo2


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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings CAGEr_2.8.0.tar.gz
StartedAt: 2024-03-01 20:34:17 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 20:50:29 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 971.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings CAGEr_2.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CAGEr.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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       31.136  3.448  34.585
clusterCTSS                30.154  0.668  30.811
exportToTrack              29.719  0.624  30.343
quantilePositions          22.566  2.156  24.722
cumulativeCTSSdistribution 19.936  4.332  24.271
scoreShift                 22.283  1.340  23.623
annotateCTSS               19.804  2.208  22.013
CustomConsensusClusters    11.047  1.164  12.210
getExpressionProfiles      10.235  0.932  11.168
plotExpressionProfiles      8.383  0.492   8.875
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CAGE_Resources.Rmd’ using ‘UTF-8’... OK
  ‘CAGEexp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CAGEr.Rcheck/00check.log’
for details.



Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-class2.8910.0882.980
CAGEr_Multicore3.3780.1603.538
CTSS-class0.2790.0240.303
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0720.0080.079
CTSSnormalizedTpm0.6590.0840.743
CTSStagCount0.7970.0920.890
CTSStoGenes0.3660.0440.410
CustomConsensusClusters11.047 1.16412.210
GeneExpDESeq20.4530.0320.484
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1390.0040.142
aggregateTagClusters31.136 3.44834.585
annotateCTSS19.804 2.20822.013
byCtss0.0160.0000.017
clusterCTSS30.154 0.66830.811
consensusClusters0.1160.0000.116
consensusClustersDESeq23.5310.4483.979
consensusClustersTpm0.0050.0000.005
coverage-functions1.6000.3201.921
cumulativeCTSSdistribution19.936 4.33224.271
distclu-functions3.4680.6734.090
exampleCAGEexp000
exportToTrack29.719 0.62430.343
expressionClasses3.2840.4203.704
genomeName000
getCTSS0.8760.0120.888
getExpressionProfiles10.235 0.93211.168
getShiftingPromoters4.510.484.99
hanabi0.2120.0040.215
hanabiPlot0.2580.0240.282
import.CAGEscanMolecule000
import.CTSS0.0750.0000.075
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule0.0000.0000.001
inputFiles0.0010.0000.001
inputFilesType0.0010.0000.002
librarySizes0.0010.0000.001
mapStats0.0510.0000.051
mergeCAGEsets1.9670.0281.994
mergeSamples0.4310.0000.431
moleculesGR2CTSS0.1290.0000.128
normalizeTagCount0.5000.0000.476
parseCAGEscanBlocksToGrangeTSS0.0220.0000.021
plotAnnot2.1600.0162.176
plotCorrelation0.2290.0000.230
plotExpressionProfiles8.3830.4928.875
plotInterquantileWidth1.8190.0671.887
plotReverseCumulatives0.3430.0030.305
quantilePositions22.566 2.15624.722
quickEnhancers000
ranges2annot0.3550.0000.356
ranges2genes0.0560.0000.056
ranges2names0.0540.0000.055
resetCAGEexp0.3130.0000.314
rowSums.RleDataFrame0.020.000.02
rowsum.RleDataFrame0.0220.0000.022
sampleLabels0.0040.0000.004
scoreShift22.283 1.34023.623
seqNameTotalsSE0.0040.0000.004
setColors0.2980.0000.299
strandInvaders0.6650.0200.664
summariseChrExpr0.4030.0010.402
tagClusters0.2170.0000.217