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This page was generated on 2025-10-17 12:07 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 164/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.4  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 Oct 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: devel
git_last_commit: 7c5727b
git_last_commit_date: 2025-10-09 09:40:05 -0400 (Thu, 09 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for benchdamic on taishan

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: 1.15.4
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_1.15.4.tar.gz
StartedAt: 2025-10-17 06:21:34 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 06:51:22 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 1788.4 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_1.15.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.15.4’
* 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: fitModels
> ### Title: fitModels
> ### Aliases: fitModels
> 
> ### ** 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 
  0.478   0.087   0.598 
After right optimization = -1207.77070452653
After orthogonalization = -1207.77070452653
   user  system elapsed 
  0.050   0.000   0.072 
After left optimization = -1204.98391365776
After orthogonalization = -1204.98391365776
Iteration 2
penalized log-likelihood = -1204.98391365776
After dispersion optimization = -1204.98391365776
   user  system elapsed 
  0.298   0.211   1.022 
After right optimization = -1203.06043616196
After orthogonalization = -1203.06043616196
   user  system elapsed 
  0.042   0.000   0.085 
After left optimization = -1202.94616837058
After orthogonalization = -1202.94616837058
Iteration 3
penalized log-likelihood = -1202.94616837058
After dispersion optimization = -1202.94616837058
   user  system elapsed 
  0.303   0.030   0.401 
After right optimization = -1202.91343811246
After orthogonalization = -1202.91343811246
   user  system elapsed 
  0.034   0.004   0.038 
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-1724.23283617012"
[1] "Iteration 4 Newton's update, log-likelihood-1653.33066927551"
[1] "Iteration 5 Newton's update, log-likelihood-1534.25649332615"
[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
createTIEC        5.412 10.569  55.403
createConcordance 7.943  0.431  15.585
areaCAT           6.369  0.481   8.342
DA_ALDEx2         4.966  0.148   5.124
createPositives   1.682  0.046   5.183
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.15.4’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 2 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 334 ]
> 
> proc.time()
    user   system  elapsed 
 100.374  275.684 1030.547 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0040.0000.004
DA_ALDEx24.9660.1485.124
DA_ANCOM1.1200.0441.167
DA_DESeq23.7370.0593.806
DA_MAST1.7680.0481.826
DA_Maaslin20.4140.0040.483
DA_NOISeq1.5050.0921.603
DA_Seurat2.4940.2872.792
DA_ZicoSeq1.0370.0881.127
DA_basic0.0480.0040.053
DA_corncob0.9390.0791.066
DA_dearseq0.0680.0200.089
DA_edgeR0.2400.0080.248
DA_limma0.1040.0040.107
DA_linda0.0640.0080.073
DA_maaslin30.8050.0800.893
DA_metagenomeSeq0.3550.0160.374
DA_mixMC1.0300.0801.114
RMSE0.0000.0000.001
addKnowledge0.2310.0160.251
areaCAT6.3690.4818.342
checkNormalization0.0010.0000.001
createColors0.0060.0000.006
createConcordance 7.943 0.43115.585
createEnrichment0.3850.0161.174
createMocks0.0030.0000.021
createPositives1.6820.0465.183
createSplits0.0440.0080.316
createTIEC 5.41210.56955.403
enrichmentTest0.1960.0210.253
extractDA0.2930.0400.334
extractStatistics0.2850.0270.314
fitDM0.0530.0000.063
fitHURDLE0.9820.3542.055