Jakob Wirbel
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/SIAMCAT |
| git_branch: RELEASE_3_22 |
| git_last_commit: cf500c9 |
| git_last_commit_date: 2025-10-29 10:45:25 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:01 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 2006/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 2.14.0 (landing page) Jakob Wirbel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: SIAMCAT |
| Version: 2.14.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SIAMCAT_2.14.0.tar.gz |
| StartedAt: 2025-12-02 04:27:53 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 04:36:21 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 508.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SIAMCAT.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SIAMCAT_2.14.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.14.0’
* 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 ... INFO
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
help 1.9Mb
* 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
assign-model_list 21.358 0.323 21.684
train.model 21.061 0.118 21.179
make.predictions 20.817 0.261 21.078
model.interpretation.plot 20.861 0.203 21.064
* 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
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/conf_assoc_plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/SIAMCAT.Rcheck/vign_test/SIAMCAT/vignettes/SIAMCAT_confounder_files/figure-html/dorea_plot-1.png" but not available.
--- finished re-building ‘SIAMCAT_confounder.Rmd’
--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown
Quitting from SIAMCAT_holdout.Rmd:54-69 [siamcat_fr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/meta_Zeller.tsv'
---
Backtrace:
▆
1. └─utils::read.table(...)
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/meta_Zeller.tsv'
--- failed re-building ‘SIAMCAT_holdout.Rmd’
--- re-building ‘SIAMCAT_meta.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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 file failed:
‘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-3.22-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.
SIAMCAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SIAMCAT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘SIAMCAT’ ... ** this is package ‘SIAMCAT’ version ‘2.14.0’ ** 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)
SIAMCAT.Rcheck/SIAMCAT-Ex.timings
| name | user | system | elapsed | |
| accessSlot | 0.005 | 0.001 | 0.007 | |
| add.meta.pred | 0.022 | 0.001 | 0.023 | |
| assign-associations | 0.005 | 0.001 | 0.005 | |
| assign-data_split | 0.004 | 0.002 | 0.006 | |
| assign-eval_data | 0.006 | 0.000 | 0.006 | |
| assign-filt_feat | 0.005 | 0.001 | 0.006 | |
| assign-label | 0.005 | 0.001 | 0.006 | |
| assign-meta | 0.024 | 0.001 | 0.025 | |
| assign-model_list | 21.358 | 0.323 | 21.684 | |
| assign-norm_feat | 0.006 | 0.000 | 0.007 | |
| assign-orig_feat | 0.009 | 0.002 | 0.011 | |
| assign-physeq | 0.005 | 0.001 | 0.007 | |
| assign-pred_matrix | 0.046 | 0.001 | 0.047 | |
| assoc_param-methods | 0.005 | 0.000 | 0.005 | |
| association.plot | 0.202 | 0.004 | 0.206 | |
| associations-methods | 0.007 | 0.000 | 0.007 | |
| check.associations | 0.007 | 0.000 | 0.008 | |
| check.confounders | 0.404 | 0.011 | 0.415 | |
| create.data.split | 0.040 | 0.004 | 0.044 | |
| create.label | 0.001 | 0.002 | 0.002 | |
| data_split-methods | 0.005 | 0.000 | 0.005 | |
| eval_data-methods | 0.006 | 0.000 | 0.006 | |
| evaluate.predictions | 2.231 | 0.062 | 2.292 | |
| feature_type-methods | 0.004 | 0.000 | 0.005 | |
| feature_weights-methods | 0.004 | 0.001 | 0.005 | |
| filt_feat-methods | 0.005 | 0.000 | 0.005 | |
| filt_params-methods | 0.005 | 0.000 | 0.004 | |
| filter.features | 0.010 | 0.002 | 0.012 | |
| filter.label | 0.005 | 0.000 | 0.006 | |
| get.filt_feat.matrix | 0.003 | 0.001 | 0.005 | |
| get.norm_feat.matrix | 0.004 | 0.001 | 0.005 | |
| get.orig_feat.matrix | 0.005 | 0.000 | 0.004 | |
| label-methods | 0.004 | 0.000 | 0.004 | |
| make.predictions | 20.817 | 0.261 | 21.078 | |
| meta-methods | 0.017 | 0.001 | 0.018 | |
| model.evaluation.plot | 0.021 | 0.002 | 0.022 | |
| model.interpretation.plot | 20.861 | 0.203 | 21.064 | |
| model_list-methods | 0.004 | 0.001 | 0.005 | |
| model_type-methods | 0.004 | 0.001 | 0.005 | |
| models-methods | 0.004 | 0.000 | 0.005 | |
| norm_feat-methods | 0.002 | 0.002 | 0.005 | |
| norm_params-methods | 0.003 | 0.001 | 0.005 | |
| normalize.features | 0.013 | 0.000 | 0.013 | |
| orig_feat-methods | 0.005 | 0.000 | 0.005 | |
| physeq-methods | 0.006 | 0.002 | 0.008 | |
| pred_matrix-methods | 0.005 | 0.000 | 0.005 | |
| read.label | 0.007 | 0.000 | 0.008 | |
| read.lefse | 0.549 | 0.013 | 0.563 | |
| select.samples | 0.050 | 0.001 | 0.051 | |
| siamcat | 0.256 | 0.008 | 0.264 | |
| siamcat.to.lefse | 0.015 | 0.000 | 0.015 | |
| siamcat.to.maaslin | 0.016 | 0.000 | 0.016 | |
| summarize.features | 1.842 | 0.073 | 1.915 | |
| train.model | 21.061 | 0.118 | 21.179 | |
| validate.data | 0.019 | 0.000 | 0.018 | |
| volcano.plot | 0.009 | 0.002 | 0.010 | |
| weight_matrix-methods | 0.005 | 0.000 | 0.004 | |