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This page was generated on 2024-02-22 11:36:35 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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: 2024-02-21 14:05:05 -0500 (Wed, 21 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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CAGEr_2.8.0.tar.gz
StartedAt: 2024-02-21 23:43:44 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 23:54:01 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 617.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CAGEr_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/CAGEr.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
clusterCTSS                30.37   0.50   30.88
aggregateTagClusters       29.56   0.89   30.45
exportToTrack              29.52   0.48   30.02
quantilePositions          24.83   0.58   25.41
annotateCTSS               24.75   0.59   25.35
cumulativeCTSSdistribution 20.67   0.92   21.60
scoreShift                 20.48   0.43   20.92
getExpressionProfiles      11.78   0.20   11.98
CustomConsensusClusters    11.61   0.24   11.84
plotExpressionProfiles      8.27   0.22    8.48
CAGEexp-class               5.08   1.67    6.82
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/CAGEr.Rcheck/00check.log'
for details.



Installation output

CAGEr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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-class5.081.676.82
CAGEr_Multicore2.360.002.36
CTSS-class0.260.000.27
CTSSclusteringMethod000
CTSScoordinates0.080.000.07
CTSSnormalizedTpm0.630.020.65
CTSStagCount0.720.140.85
CTSStoGenes0.400.040.46
CustomConsensusClusters11.61 0.2411.84
GeneExpDESeq20.500.010.52
GeneExpSE0.020.000.01
QuantileWidthFunctions0.170.000.17
aggregateTagClusters29.56 0.8930.45
annotateCTSS24.75 0.5925.35
byCtss0.020.000.01
clusterCTSS30.37 0.5030.88
consensusClusters0.100.020.11
consensusClustersDESeq23.760.053.81
consensusClustersTpm000
coverage-functions1.780.141.92
cumulativeCTSSdistribution20.67 0.9221.60
distclu-functions3.080.143.21
exampleCAGEexp000
exportToTrack29.52 0.4830.02
expressionClasses4.440.114.55
genomeName000
getCTSS0.980.051.03
getExpressionProfiles11.78 0.2011.98
getShiftingPromoters4.250.164.41
hanabi0.220.020.23
hanabiPlot0.280.020.30
import.CAGEscanMolecule000
import.CTSS0.090.000.09
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles000
inputFilesType000
librarySizes000
mapStats0.030.010.05
mergeCAGEsets2.280.002.28
mergeSamples0.550.000.55
moleculesGR2CTSS0.120.000.12
normalizeTagCount0.550.000.55
parseCAGEscanBlocksToGrangeTSS0.010.000.01
plotAnnot2.250.082.33
plotCorrelation0.220.020.24
plotExpressionProfiles8.270.228.48
plotInterquantileWidth1.790.001.80
plotReverseCumulatives0.300.010.31
quantilePositions24.83 0.5825.41
quickEnhancers000
ranges2annot0.310.010.32
ranges2genes0.060.000.07
ranges2names0.070.000.06
resetCAGEexp0.260.040.30
rowSums.RleDataFrame0.020.000.01
rowsum.RleDataFrame0.010.000.02
sampleLabels0.020.000.01
scoreShift20.48 0.4320.92
seqNameTotalsSE000
setColors0.390.000.39
strandInvaders0.790.131.71
summariseChrExpr0.450.000.46
tagClusters0.220.000.22