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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1708/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recoup 1.34.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/recoup
git_branch: RELEASE_3_20
git_last_commit: 0a61aae
git_last_commit_date: 2024-10-29 10:08:59 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for recoup on kjohnson1

To the developers/maintainers of the recoup package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recoup.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: recoup
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.34.0.tar.gz
StartedAt: 2024-12-21 06:16:37 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 06:24:04 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 446.7 seconds
RetCode: 0
Status:   OK  
CheckDir: recoup.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/recoup.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recoup/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘recoup’ version ‘1.34.0’
* 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 ‘recoup’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’
  ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘biomaRt:::martVSchema’ ‘txdbmaker:::GFF_FEATURE_TYPES’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeHorizontalAnnotation’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readBamIntervals: no visible binding for global variable ‘bam.file’
recoupCorrelation: no visible binding for global variable ‘Index’
recoupCorrelation: no visible binding for global variable ‘Coverage’
recoupCorrelation: no visible binding for global variable ‘Condition’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
  ‘grid.text’
recoupProfile: no visible binding for global variable ‘Signal’
recoupProfile: no visible binding for global variable ‘Condition’
recoupProfile: no visible binding for global variable ‘Design’
Undefined global functions or variables:
  Condition Coverage Design Index Signal bam.file grid.text
* checking Rd files ... NOTE
checkRd: (-1) recoup.Rd:210-211: Lost braces
   210 |     \code{region}{Minimum flank is 0bp and maximum is
       |                  ^
* 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 ... OK
* 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
mergeRuns         20.074  0.617  20.808
profileMatrix     15.769  0.718  16.532
recoup             8.432  0.300   8.756
kmeansDesign       8.214  0.296   8.529
recoupPlot         7.509  0.231   7.768
simpleGetSet       7.408  0.225   7.658
sliceObj           7.244  0.268   7.543
recoupCorrelation  6.033  0.201   6.250
recoupHeatmap      5.834  0.171   6.018
recoupProfile      5.834  0.162   6.019
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/recoup.Rcheck/00check.log’
for details.


Installation output

recoup.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recoup
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘recoup’ ...
** 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 (recoup)

Tests output

recoup.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("recoup")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'grid'

The following object is masked from 'package:Biostrings':

    pattern

========================================
ComplexHeatmap version 2.22.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

Getting main ranges for measurements
  measurement type: chipseq
  genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
  calculating total coverage
  processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
  calculating total coverage
  processing chr12
Calculating profile for WT H4K20me1
Calculating profile for Set8KO H4K20me1
Constructing genomic coverage profile curve(s)
The resolution of the requested profiles will be lowered to avoid
increased computation time and/or storage space for heatmap profiles...
Calculating tss profile for WT H4K20me1
Calculating tss profile for Set8KO H4K20me1
Constructing genomic coverage heatmap(s)
Constructing coverage correlation profile curve(s)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Getting main ranges for measurements
  measurement type: chipseq
  genomic region type: genebody
Calculating requested regions coverage for WT H4K20me1
  calculating total coverage
  processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
  calculating total coverage
  processing chr12
Calculating profile for WT H4K20me1
 center
 upstream
 downstream
Calculating profile for Set8KO H4K20me1
 center
 upstream
 downstream
Constructing genomic coverage profile curve(s)
Using provided design to facet the coverage profiles
Constructing genomic coverage heatmap(s)
Using provided design to facet the coverage profiles
Constructing coverage correlation profile curve(s)
Using provided design to facet the coverage profiles
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")


RUNIT TEST PROTOCOL -- Sat Dec 21 06:23:55 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
recoup RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 38.469   1.631  40.249 

Example timings

recoup.Rcheck/recoup-Ex.timings

nameusersystemelapsed
buildAnnotationDatabase000
buildAnnotationStore000
buildCustomAnnotation2.1660.0902.263
calcCoverage3.6830.0353.724
coverageRef4.6960.0794.792
coverageRnaRef000
getAnnotation1.4150.0902.002
getBiotypes0.0000.0010.000
getInstalledAnnotations0.0010.0000.002
importCustomAnnotation0.6100.0070.619
kmeansDesign8.2140.2968.529
loadAnnotation0.0010.0010.001
mergeRuns20.074 0.61720.808
preprocessRanges0.2580.0250.288
profileMatrix15.769 0.71816.532
recoup8.4320.3008.756
recoupCorrelation6.0330.2016.250
recoupHeatmap5.8340.1716.018
recoupPlot7.5090.2317.768
recoupProfile5.8340.1626.019
removeData0.0180.0010.021
rpMatrix0.5870.0090.596
simpleGetSet7.4080.2257.658
sliceObj7.2440.2687.543