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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 333/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.26.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_19
git_last_commit: 0c3fa2c
git_last_commit_date: 2024-04-30 11:00:14 -0400 (Tue, 30 Apr 2024)
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
merida1macOS 12.7.4 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 ChIPanalyser on palomino3

To the developers/maintainers of the ChIPanalyser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPanalyser.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: ChIPanalyser
Version: 1.26.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPanalyser_1.26.0.tar.gz
StartedAt: 2024-06-17 01:42:59 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 01:50:18 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 438.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPanalyser_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ChIPanalyser.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'ChIPanalyser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPanalyser' version '1.26.0'
* 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 'ChIPanalyser' 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) data.Rd:24-25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:26-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:28-31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:32-33: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:34-35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) evolve.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:93-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateStartingPopulation.Rd:31-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) generateStartingPopulation.Rd:40-44: Lost braces in \enumerate; 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 ... 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 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 '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: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/ChIPanalyser.Rcheck/00check.log'
for details.


Installation output

ChIPanalyser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'ChIPanalyser' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'drop' in package 'ChIPanalyser'
** 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 (ChIPanalyser)

Tests output

ChIPanalyser.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24 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.

> BiocGenerics:::testPackage("ChIPanalyser")

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


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: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'rtracklayer'

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

    FileForFormat


Attaching package: 'ChIPanalyser'

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

    drop

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

    drop

Loading required package: BSgenome.Dmelanogaster.UCSC.dm6


RUNIT TEST PROTOCOL -- Mon Jun 17 01:49:59 2024 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPanalyser RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  87.53   35.31  125.32 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.310.000.31
BPFrequency_-0.000.010.01
ChIPScore-class0.010.000.02
ChIPanalyser-package000
DNASequenceLength000
GRList-class000
PFMFormat0.200.030.24
PFMFormat_0.070.000.06
PWMThreshold0.000.020.02
PWMThreshold_-0.000.020.01
PWMpseudocount0.000.010.02
PWMpseudocount_-0.000.030.03
PositionFrequencyMatrix0.040.030.08
PositionFrequencyMatrix_-0.020.020.03
PositionWeightMatrix0.080.020.09
PositionWeightMatrix_-0.030.000.03
averageExpPWMScore0.040.010.07
backgroundSignal0.020.000.01
backgroundSignal_-0.000.020.02
boundMolecules0.000.010.01
boundMolecules_-0.020.000.02
chipMean000
chipMean_-000
chipSd0.000.020.02
chipSd_-0.020.000.02
chipSmooth000
chipSmooth_-0.010.000.01
computeChIPProfile0.000.010.02
computeGenomeWideScores000
computeOccupancy0.000.020.01
computeOptimal0.020.000.02
computePWMScore0.010.000.01
data000
drop0.080.000.08
evolve000
generateStartingPopulation0.040.000.04
genomicProfiles-class000
genomicProfiles0.970.031.00
genomicProfilesInternal-class000
getHighestFitnessSolutions0.000.020.02
getTestingData3.920.204.30
getTrainingData1.290.171.50
lambdaPWM0.020.000.02
lambdaPWM_0.010.000.01
loci-class000
loci1.320.171.55
lociWidth0.000.020.02
lociWidth_0.010.000.01
maxPWMScore000
maxSignal0.020.000.01
maxSignal_-000
minPWMScore0.000.010.02
naturalLog0.000.040.03
naturalLog_-000
noOfSites0.000.010.02
noOfSites_-0.000.020.01
noiseFilter0.010.000.02
noiseFilter_0.010.000.02
nos-class000
parameterOptions-class000
parameterOptions0.000.010.01
ploidy000
ploidy_-0.020.000.02
plotOccupancyProfile000
plotOptimalHeatMaps0.010.000.01
processingChIP1.190.141.36
profileAccuracyEstimate0.000.020.02
removeBackground0.020.000.02
removeBackground_-000
scores1.210.191.41
searchSites0.010.000.01
setChromatinStates1.420.041.46
singleRun0.020.000.01
splitData1.410.161.60
stepSize000
stepSize_-0.020.000.02
strandRule0.010.010.03
strandRule_-0.000.020.01
whichstrand0.000.020.02
whichstrand_-0.000.010.01