Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 164/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
betaHMM 1.4.2  (landing page)
Koyel Majumdar
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/betaHMM
git_branch: RELEASE_3_21
git_last_commit: 414edca
git_last_commit_date: 2025-09-22 14:16:09 -0400 (Mon, 22 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for betaHMM on kunpeng2

To the developers/maintainers of the betaHMM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/betaHMM.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: betaHMM
Version: 1.4.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:betaHMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings betaHMM_1.4.2.tar.gz
StartedAt: 2025-10-10 06:29:03 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 06:41:12 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 729.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: betaHMM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:betaHMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings betaHMM_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/betaHMM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘betaHMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘betaHMM’ version ‘1.4.2’
* 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 ‘betaHMM’ 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 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘betaHMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Visualize results from 'betaHMM'/ 'dmc_identification'/
> ###   'threshold_identification' functions.
> ### Aliases: plot plot,betaHMMResults-method plot-methods
> ###   plot,dmcResults-method plot,threshold_Results-method
> 
> ### ** Examples
> 
> ## Use simulated data for the betaHMM workflow example
> set.seed(12345)
> 
> ## read files
> data(sample_methylation_file)
> data(sample_annotation_file)
> # Run betaHMM function
> beta_out <- betaHMM(sample_methylation_file[1:50,],
+                     sample_annotation_file[1:50,],
+                     M = 3, N = 4, R = 2,iterations=2,
+                     parallel_process = FALSE, seed = 12345,
+                     treatment_group = c("Benign","Tumour"))
> 
> ## Run dmc_identification function
> dmc_out <- dmc_identification(beta_out)
> 
> # Run dmr_identification function
> dmr_out <- dmr_identification(dmc_out, parallel_process = FALSE)
> 
> # Plot functions
> # Get the AUC values calculated for each hidden state
> AUC_chr <- AUC(dmc_out)
> 
> ## plot the uncertainty for each hidden state
> plot(beta_out, chromosome = "1", what = "uncertainty")
> 
> ## Use simulated data for the betaHMM workflow example
> set.seed(12345)
> 
> ## read files
> data(sample_methylation_file)
> data(sample_annotation_file)
> # Run betaHMM function
> beta_out <- betaHMM(sample_methylation_file[1:50,],
+                     sample_annotation_file[1:50,],
+                     M = 3, N = 4, R = 2,iterations=2,
+                     parallel_process = FALSE, seed = 12345,
+                     treatment_group = c("Benign","Tumour"))
Error in serverSocket(port = port) : 
  creation of server socket failed: port 11098 cannot be opened
Calls: betaHMM ... betaHMMrun -> makeCluster -> makePSOCKcluster -> serverSocket
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
betaHMM                2.062  0.707  25.233
betaHMMResults         1.196  0.166  23.853
dmrResults             0.909  0.169  23.749
dmr_identification     0.893  0.129  24.349
packageHelpers         0.905  0.114  24.318
dmcResults             0.913  0.104  23.428
dmc_identification     0.927  0.076  24.020
dmc_identification_run 0.869  0.115  23.456
betaHMMrun             0.871  0.074  23.367
dmr_identification_run 0.852  0.092  23.697
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 3655729 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  The following object is masked from 'package:stats4':
  
      plot
  
  The following object is masked from 'package:graphics':
  
      plot
  
  The following object is masked from 'package:base':
  
      plot
  
  > 
  > test_check("betaHMM")
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/betaHMM.Rcheck/00check.log’
for details.


Installation output

betaHMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL betaHMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘betaHMM’ ...
** this is package ‘betaHMM’ version ‘1.4.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘plot’ in package ‘betaHMM’
** 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 (betaHMM)

Tests output

betaHMM.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(betaHMM)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

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
Loading required package: GenomeInfoDb
Loading required package: Biobase
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: 'betaHMM'

The following object is masked from 'package:stats4':

    plot

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

    plot

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

    plot

> 
> test_check("betaHMM")

Example timings

betaHMM.Rcheck/betaHMM-Ex.timings

nameusersystemelapsed
betaHMM 2.062 0.70725.233
betaHMMResults 1.196 0.16623.853
betaHMMrun 0.871 0.07423.367
dmcResults 0.913 0.10423.428
dmc_identification 0.927 0.07624.020
dmc_identification_run 0.869 0.11523.456
dmrResults 0.909 0.16923.749
dmr_identification 0.893 0.12924.349
dmr_identification_run 0.852 0.09223.697
packageHelpers 0.905 0.11424.318