Build/check report for BioC 3.23 - CHECK results for SIAMCAT on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4995
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*

CHECK results for SIAMCAT on nebbiolo1

To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.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: SIAMCAT

Version: 2.16.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SIAMCAT_2.16.0.tar.gz

StartedAt: 2026-05-26 04:55:06 -0400 (Tue, 26 May 2026)

EndedAt: 2026-05-26 05:03:35 -0400 (Tue, 26 May 2026)

EllapsedTime: 509.0 seconds

RetCode: 1

Status: ERROR

CheckDir: SIAMCAT.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SIAMCAT_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-26 08:55:07 UTC
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SIAMCAT’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.associations.Rd: lmerTest
  summarize.features.Rd: phyloseq
  train.model.Rd: mlr3learners, glmnet, LiblineaR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
model.interpretation.plot 24.315  0.261  24.576
assign-model_list         23.272  0.418  23.693
train.model               23.350  0.164  23.516
make.predictions          23.240  0.088  23.330
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SIAMCAT_confounder.Rmd’ using rmarkdown

Quitting from SIAMCAT_confounder.Rmd:159-179 [load_motus]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─readr::read_tsv(paste0(data.loc, "meta_Nielsen.tsv"))
 2. │ └─vroom::vroom(...)
 3. │   └─vroom:::vroom_(...)
 4. └─vroom (local) `<fn>`(`<curl>`, "rb")
 5.   └─base::tryCatch(...)
 6.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_confounder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SIAMCAT_confounder.Rmd’

--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown

Quitting from SIAMCAT_holdout.Rmd:74-87 [siamcat_cn]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/specI_Yu.tsv'
---
Backtrace:
    ▆
 1. └─utils::read.table(fn.feat.cn, sep = "\t", quote = "", check.names = FALSE)
 2.   └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_holdout.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/specI_Yu.tsv'
--- failed re-building ‘SIAMCAT_holdout.Rmd’

--- re-building ‘SIAMCAT_meta.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/plot_auroc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_meta_files/figure-html/plot_weights_heatmap-1.png" but not available.
--- finished re-building ‘SIAMCAT_meta.Rmd’

--- re-building ‘SIAMCAT_ml_pitfalls.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_auroc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/hmp_samples-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_ml_pitfalls_files/figure-html/plot_results_db-1.png" but not available.
--- finished re-building ‘SIAMCAT_ml_pitfalls.Rmd’

--- re-building ‘SIAMCAT_read-in.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_read-in.Rmd’

--- re-building ‘SIAMCAT_vignette.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘SIAMCAT_confounder.Rmd’ ‘SIAMCAT_holdout.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SIAMCAT’ ...
** this is package ‘SIAMCAT’ version ‘2.16.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (SIAMCAT)

Tests output

Example timings

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

name	user	system	elapsed
accessSlot	0.007	0.003	0.009
add.meta.pred	0.025	0.000	0.025
assign-associations	0.007	0.000	0.007
assign-data_split	0.006	0.001	0.007
assign-eval_data	0.022	0.001	0.023
assign-filt_feat	0.005	0.000	0.006
assign-label	0.005	0.001	0.006
assign-meta	0.026	0.000	0.026
assign-model_list	23.272	0.418	23.693
assign-norm_feat	0.005	0.000	0.007
assign-orig_feat	0.011	0.000	0.011
assign-physeq	0.006	0.001	0.006
assign-pred_matrix	0.005	0.002	0.007
assoc_param-methods	0.004	0.001	0.006
association.plot	0.206	0.006	0.213
associations-methods	0.009	0.000	0.008
check.associations	0.007	0.002	0.010
check.confounders	0.426	0.005	0.431
create.data.split	0.021	0.001	0.021
create.label	0.002	0.000	0.003
data_split-methods	0.004	0.000	0.005
eval_data-methods	0.005	0.001	0.005
evaluate.predictions	1.738	0.000	1.738
feature_type-methods	0.004	0.000	0.006
feature_weights-methods	0.003	0.001	0.006
filt_feat-methods	0.005	0.000	0.006
filt_params-methods	0.005	0.000	0.005
filter.features	0.011	0.001	0.012
filter.label	0.005	0.001	0.006
get.filt_feat.matrix	0.004	0.001	0.005
get.norm_feat.matrix	0.005	0.000	0.005
get.orig_feat.matrix	0.004	0.001	0.005
label-methods	0.004	0.001	0.006
make.predictions	23.240	0.088	23.330
meta-methods	0.023	0.004	0.027
model.evaluation.plot	0.052	0.003	0.055
model.interpretation.plot	24.315	0.261	24.576
model_list-methods	0.004	0.001	0.005
model_type-methods	0.004	0.001	0.005
models-methods	0.005	0.000	0.005
norm_feat-methods	0.004	0.001	0.005
norm_params-methods	0.003	0.000	0.005
normalize.features	0.013	0.001	0.013
orig_feat-methods	0.005	0.001	0.006
physeq-methods	0.007	0.002	0.009
pred_matrix-methods	0.005	0.000	0.005
read.label	0.005	0.002	0.007
read.lefse	0.590	0.022	0.614
select.samples	0.051	0.003	0.054
siamcat	0.300	0.007	0.307
siamcat.to.lefse	0.015	0.001	0.016
siamcat.to.maaslin	0.016	0.001	0.018
summarize.features	1.760	0.065	1.826
train.model	23.350	0.164	23.516
validate.data	0.018	0.001	0.019
volcano.plot	0.009	0.002	0.011
weight_matrix-methods	0.004	0.001	0.005