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This page was generated on 2024-03-28 11:36:15 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.9.0.tar.gz
StartedAt: 2024-03-27 20:52:33 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:08:58 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 984.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 ‘2.9.0’
* 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 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 ... 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
aggregateTagClusters       29.921  3.184  33.107
exportToTrack              29.411  0.452  29.864
clusterCTSS                28.976  0.468  29.435
cumulativeCTSSdistribution 18.365  4.280  22.645
scoreShift                 20.961  1.316  22.278
annotateCTSS               19.528  2.088  21.617
quantilePositions          18.423  2.072  20.496
CustomConsensusClusters    10.844  0.848  11.692
getExpressionProfiles       8.135  0.848   8.983
plotExpressionProfiles      8.308  0.543   8.852
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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-class1.7710.0641.839
CAGEr_Multicore3.2030.0043.207
CTSS-class0.2430.0080.251
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0670.0000.067
CTSSnormalizedTpm0.6410.0270.668
CTSStagCount0.7270.1320.858
CTSStoGenes0.3280.0560.383
CustomConsensusClusters10.844 0.84811.692
GeneExpDESeq20.4780.0000.478
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1220.0000.122
aggregateTagClusters29.921 3.18433.107
annotateCTSS19.528 2.08821.617
byCtss0.0170.0000.017
clusterCTSS28.976 0.46829.435
consensusClusters0.1180.0040.122
consensusClustersDESeq23.7670.4764.244
consensusClustersTpm0.0060.0000.006
coverage-functions1.5790.4402.019
cumulativeCTSSdistribution18.365 4.28022.645
distclu-functions3.4910.6604.106
exampleCAGEexp000
exportToTrack29.411 0.45229.864
expressionClasses3.1780.4043.581
genomeName000
getCTSS0.8790.0040.883
getExpressionProfiles8.1350.8488.983
getShiftingPromoters3.1960.4163.612
hanabi0.2040.0080.212
hanabiPlot0.2530.0320.285
import.CAGEscanMolecule0.0000.0000.001
import.CTSS0.0740.0000.075
import.bam000
import.bedCTSS000
import.bedScore0.0000.0000.001
import.bedmolecule000
inputFiles0.0000.0010.001
inputFilesType0.0010.0010.001
librarySizes0.0010.0000.001
mapStats0.0470.0040.051
mergeCAGEsets1.8580.0481.907
mergeSamples0.4270.0160.443
moleculesGR2CTSS0.1420.0040.146
normalizeTagCount0.4550.0040.437
parseCAGEscanBlocksToGrangeTSS0.0210.0000.021
plotAnnot2.1700.0082.179
plotCorrelation0.2350.0000.236
plotExpressionProfiles8.3080.5438.852
plotInterquantileWidth1.7690.0041.774
plotReverseCumulatives0.3250.0040.288
quantilePositions18.423 2.07220.496
quickEnhancers000
ranges2annot0.3480.0000.348
ranges2genes0.0570.0000.057
ranges2names0.0510.0040.054
resetCAGEexp0.3050.0040.308
rowSums.RleDataFrame0.0210.0000.021
rowsum.RleDataFrame0.0200.0040.024
sampleLabels0.0040.0000.004
scoreShift20.961 1.31622.278
seqNameTotalsSE0.0040.0000.004
setColors0.2790.0000.280
strandInvaders0.6610.1070.748
summariseChrExpr0.3730.0000.372
tagClusters0.2170.0040.221