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This page was generated on 2024-05-22 11:37:10 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4400
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
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 1584/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.41.0  (landing page)
Diego Diez
Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/PWMEnrich
git_branch: devel
git_last_commit: 2998058
git_last_commit_date: 2024-04-30 10:28:05 -0400 (Tue, 30 Apr 2024)
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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for PWMEnrich on palomino4


To the developers/maintainers of the PWMEnrich package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PWMEnrich.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: PWMEnrich
Version: 4.41.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PWMEnrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PWMEnrich_4.41.0.tar.gz
StartedAt: 2024-05-21 03:52:55 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 03:54:52 -0400 (Tue, 21 May 2024)
EllapsedTime: 116.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PWMEnrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PWMEnrich_4.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/PWMEnrich.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PWMEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PWMEnrich' version '4.41.0'
* 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 'PWMEnrich' 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 ... 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) plot-MotifEnrichmentReport-missing-method.Rd:31-47: Lost braces
    31 | if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
       |                                                           ^
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-all.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: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/PWMEnrich.Rcheck/00check.log'
for details.


Installation output

PWMEnrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL PWMEnrich
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'PWMEnrich' ...
** using staged installation
** R
** 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 (PWMEnrich)

Tests output

PWMEnrich.Rcheck/tests/test-all.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> library(testthat)
> library(PWMEnrich)
Loading required package: BiocGenerics

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, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_package("PWMEnrich")
No installed testthat tests found for PWMEnrich
> 
> 
> proc.time()
   user  system elapsed 
   3.31    0.25    3.53 

Example timings

PWMEnrich.Rcheck/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM000
PWMUnscaled0.930.051.02
getBackgroundFrequencies000
groupReport-MotifEnrichmentResults-method2.310.122.46
makeBackground0.020.000.01
makePWMCutoffBackground000
makePWMEmpiricalBackground000
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors000
motifDiffEnrichment2.040.002.05
motifEnrichment2.970.043.00
motifIC0.070.000.06
motifRankingForGroup-MotifEnrichmentResults-method2.120.012.14
motifRankingForSequence-MotifEnrichmentResults-method2.030.022.04
motifScores3.750.043.80
motifSimilarity0.060.000.06
plot-PWM-missing-method0.170.030.21
plotMotifScores0.060.020.08
plotTopMotifsGroup-MotifEnrichmentResults-method1.740.001.73
plotTopMotifsSequence-MotifEnrichmentResults-method1.640.031.67
readMotifs0.060.020.08
registerCoresPWMEnrich000
reverseComplement-PWM-method0.000.010.02
scanWithPWM0.030.020.04
sequenceReport-MotifEnrichmentResults-method2.210.112.31
toPWM000
useBigMemoryPWMEnrich000