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This page was generated on 2023-11-02 11:40:31 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 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 329/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.24.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_18
git_last_commit: c88afcb
git_last_commit_date: 2023-10-24 10:59:22 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for ChIPanalyser on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ChIPanalyser
Version: 1.24.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ChIPanalyser_1.24.0.tar.gz
StartedAt: 2023-11-02 09:11:48 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 09:18:13 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 385.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ChIPanalyser.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ChIPanalyser_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.24.0’
* 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 ‘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 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 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 ... 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 ... 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 ... ERROR
Running examples in ‘ChIPanalyser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: splitData
> ### Title: Get Training and Testing data from ChIPscore objects
> ### Aliases: splitData
> 
> ### ** Examples
> 
> 
> library(ChIPanalyser)
> data(ChIPanalyserData)
> # See GA vignette for usage 
> test <- processingChIP(chip,top)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 508023 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
      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
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.


Installation output

ChIPanalyser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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, sort, 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: '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

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.2040.0070.251
BPFrequency_-0.0020.0000.002
ChIPScore-class0.0010.0000.001
ChIPanalyser-package000
DNASequenceLength0.0020.0000.002
GRList-class0.0010.0000.001
PFMFormat0.2280.0200.249
PFMFormat_0.0660.0040.070
PWMThreshold0.0100.0040.014
PWMThreshold_-0.0130.0000.014
PWMpseudocount0.0070.0070.013
PWMpseudocount_-0.0140.0000.014
PositionFrequencyMatrix0.0620.0090.071
PositionFrequencyMatrix_-0.0340.0030.036
PositionWeightMatrix0.050.020.07
PositionWeightMatrix_-0.0160.0040.021
averageExpPWMScore0.0630.0080.071
backgroundSignal0.0080.0040.012
backgroundSignal_-0.0140.0040.018
boundMolecules0.0130.0000.013
boundMolecules_-0.0100.0080.016
chipMean0.0130.0000.013
chipMean_-0.0080.0040.013
chipSd0.0080.0040.013
chipSd_-0.0120.0000.013
chipSmooth0.0080.0040.013
chipSmooth_-0.0090.0040.013
computeChIPProfile0.0020.0000.002
computeGenomeWideScores0.0010.0000.000
computeOccupancy0.0020.0000.002
computeOptimal0.0020.0000.002
computePWMScore0.0020.0000.002
data0.0010.0000.001
drop0.0570.0120.069
evolve0.0020.0000.001
generateStartingPopulation0.0280.0000.027
genomicProfiles-class0.0010.0000.001
genomicProfiles0.0860.0120.097
genomicProfilesInternal-class0.0000.0000.001
getHighestFitnessSolutions0.0000.0010.001
getTestingData4.7480.1494.917
getTrainingData1.5750.0281.611
lambdaPWM0.0100.0030.015
lambdaPWM_0.0100.0040.014
loci-class0.0010.0000.001
loci1.5722.2065.788
lociWidth0.0060.0110.025
lociWidth_0.0140.0000.013
maxPWMScore0.0030.0000.004
maxSignal0.0120.0000.012
maxSignal_-0.0120.0000.013
minPWMScore0.0020.0000.003
naturalLog0.0090.0040.013
naturalLog_-0.0150.0000.016
noOfSites0.0130.0000.013
noOfSites_-0.0130.0000.013
noiseFilter0.0130.0000.013
noiseFilter_0.0120.0000.012
nos-class0.0010.0000.001
parameterOptions-class0.0010.0000.001
parameterOptions0.0160.0000.016
ploidy0.0120.0000.012
ploidy_-0.0110.0030.013
plotOccupancyProfile0.0020.0000.002
plotOptimalHeatMaps0.0020.0000.002
processingChIP1.5500.0651.627
profileAccuracyEstimate0.0030.0000.019
removeBackground0.0120.0000.011
removeBackground_-0.0090.0040.012
scores1.5610.0541.639
searchSites0.0030.0010.007
setChromatinStates2.3130.0072.325
singleRun0.0010.0000.002