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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 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 162/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.14.4  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_21
git_last_commit: 822521d
git_last_commit_date: 2025-10-09 09:36:33 -0400 (Thu, 09 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for benchdamic on kunpeng2

To the developers/maintainers of the benchdamic package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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: benchdamic
Version: 1.14.4
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.14.4.tar.gz
StartedAt: 2025-10-14 06:34:38 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 06:58:38 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 1439.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: benchdamic.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.14.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.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 ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.14.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘benchdamic’ 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 ... NOTE
Namespace in Imports field not imported from: ‘microbiome’
  All declared Imports should be used.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'norm_DESeq2.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ‘benchdamic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMD
> ### Title: plotMD
> ### Aliases: plotMD
> 
> ### ** Examples
> 
> # Generate some random counts
> counts = matrix(rnbinom(n = 600, size = 3, prob = 0.5), nrow = 100, ncol = 6)
> 
> # Estimate the counts assuming several distributions
> GOF <- fitModels(
+     object = counts, models = c(
+         "NB", "ZINB",
+         "DM", "ZIG", "HURDLE"
+     ), scale_HURDLE = c("median", "default")
+ )
Model: Negative Binomial
Estimating dispersions
Using classic mode.
Model: Zero-Inflated Negative Binomial
Create model:
ok
Initialize parameters:
ok
Optimize parameters:
Iteration 1
penalized log-likelihood = -1347.76278210063
After dispersion optimization = -1244.63583478121
   user  system elapsed 
  0.374   0.020   0.400 
After right optimization = -1207.77070452653
After orthogonalization = -1207.77070452653
   user  system elapsed 
  0.036   0.004   0.041 
After left optimization = -1204.98391365776
After orthogonalization = -1204.98391365776
Iteration 2
penalized log-likelihood = -1204.98391365776
After dispersion optimization = -1204.98391365776
   user  system elapsed 
  0.344   0.044   0.391 
After right optimization = -1203.06043616196
After orthogonalization = -1203.06043616196
   user  system elapsed 
  0.041   0.008   0.049 
After left optimization = -1202.94616837058
After orthogonalization = -1202.94616837058
Iteration 3
penalized log-likelihood = -1202.94616837058
After dispersion optimization = -1202.94616837058
   user  system elapsed 
  0.297   0.031   0.335 
After right optimization = -1202.91343811246
After orthogonalization = -1202.91343811246
   user  system elapsed 
  0.045   0.004   0.073 
After left optimization = -1202.90041668469
After orthogonalization = -1202.90041668469
Iteration 4
penalized log-likelihood = -1202.90041668469
ok
Model: Dirichlet Multinomial
Warning in MGLM::MGLMreg.fit(Y = data, X = X, dist = "DM", display = verbose) :
  Sample size is smaller than the number of parameters.

[1] "Iteration 2 Newton's update, log-likelihood-1981.72940248219"
[1] "Iteration 3 Newton's update, log-likelihood-1724.23283617011"
[1] "Iteration 4 Newton's update, log-likelihood-1653.33066927543"
[1] "Iteration 5 Newton's update, log-likelihood-1534.25649332612"
[1] "Iteration 6 Newton's update, log-likelihood-1286.79535867652"
[1] "Iteration 7 Newton's update, log-likelihood-1230.06023319365"
[1] "Iteration 8 Newton's update, log-likelihood-1208.93424429382"
[1] "Iteration 9 Newton's update, log-likelihood-1208.3955918424"
[1] "Iteration 10 Newton's update, log-likelihood-1208.39188601233"
Model: Zero-Inflated Gaussian
Default value being used.
it= 0, nll=10.71, log10(eps+1)=Inf, stillActive=100
it= 1, nll=11.26, log10(eps+1)=0.12, stillActive=15
it= 2, nll=11.36, log10(eps+1)=0.01, stillActive=0
Model: Truncated Gaussian Hurdle
The counts provided have been rescaled and log2 transformed.
Making a SingleCellExperiment:
No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
Assuming data assay in position 1, with name et is log-transformed.
Model: Truncated Gaussian Hurdle
The counts provided have been rescaled and log2 transformed.
Making a SingleCellExperiment:
No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
Assuming data assay in position 1, with name et is log-transformed.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotConcordance   7.076  0.096   7.242
createConcordance 6.992  0.040   7.060
areaCAT           5.747  0.119   5.915
plotLogP          4.260  1.560  15.928
plotKS            4.213  0.035   9.047
plotContingency   3.980  0.124   7.583
plotFDR           3.978  0.036   8.163
plotFPR           3.899  0.056   5.950
plotEnrichment    2.242  0.020   5.047
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck/00check.log’
for details.


Installation output

benchdamic.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.14.4’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package can be loaded from final location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package keeps a record of temporary installation path
* DONE (benchdamic)

Tests output

benchdamic.Rcheck/tests/testthat.Rout


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.

> library(testthat)
> library(benchdamic)
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
> 
> test_check("benchdamic")
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
102.455 159.577 697.370 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0040.0000.004
DA_ALDEx24.2880.2154.527
DA_ANCOM1.2040.0121.220
DA_DESeq24.2050.0364.252
DA_MAST1.9230.0481.976
DA_Maaslin20.3330.0080.360
DA_NOISeq1.7750.0961.877
DA_Seurat2.5000.0722.580
DA_ZicoSeq1.0490.0161.069
DA_basic0.0430.0000.043
DA_corncob0.9300.0081.228
DA_dearseq0.0750.0000.077
DA_edgeR0.2430.0040.248
DA_limma0.1010.0000.105
DA_linda0.0680.0160.087
DA_maaslin30.8280.0070.898
DA_metagenomeSeq0.3570.0120.371
DA_mixMC0.9870.0080.999
RMSE0.0010.0000.001
addKnowledge0.2230.0080.232
areaCAT5.7470.1195.915
checkNormalization000
createColors0.0050.0000.005
createConcordance6.9920.0407.060
createEnrichment0.4110.0120.424
createMocks0.0030.0000.003
createPositives1.3800.0001.386
createSplits0.0450.0000.045
createTIEC4.4190.0354.480
enrichmentTest0.1630.0030.167
extractDA0.2450.0000.246
extractStatistics0.2450.0000.245
fitDM0.0440.0000.044
fitHURDLE0.9090.0160.927
fitModels3.1880.0083.203
fitNB0.0590.0000.059
fitZIG0.0690.0000.069
fitZINB0.6110.0080.620
getDA0.0980.0080.107
getPositives0.1080.0000.109
getStatistics0.1500.0080.172
get_counts_metadata0.1480.0000.149
iterative_ordering0.0120.0000.012
meanDifferences0.0020.0000.002
norm_CSS0.0930.0000.093
norm_DESeq20.5790.0080.588
norm_TSS0.0490.0000.049
norm_edgeR0.0560.0000.056
plotConcordance7.0760.0967.242
plotContingency3.9800.1247.583
plotEnrichment2.2420.0205.047
plotFDR3.9780.0368.163
plotFPR3.8990.0565.950
plotKS4.2130.0359.047
plotLogP 4.260 1.56015.928