Multiple platform build/check report for BioC 3.20 - CHECK results for SIAMCAT on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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 kjohnson1

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: 2.10.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.10.0.tar.gz

StartedAt: 2025-03-19 09:15:39 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 09:20:49 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 310.7 seconds

RetCode: 0

Status: OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.10.0’
* 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 ... NOTE
  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 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 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
make.predictions          26.171  0.392  26.773
assign-model_list         25.916  0.476  26.553
model.interpretation.plot 25.384  0.430  26.169
train.model               24.852  0.412  25.749
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SIAMCAT’ ...
** 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	0.009	0.005	0.014
add.meta.pred	0.601	0.003	0.606
assign-associations	0.007	0.002	0.009
assign-data_split	0.008	0.002	0.009
assign-eval_data	0.007	0.002	0.009
assign-filt_feat	0.007	0.002	0.009
assign-label	0.007	0.002	0.009
assign-meta	0.025	0.002	0.027
assign-model_list	25.916	0.476	26.553
assign-norm_feat	0.006	0.002	0.009
assign-orig_feat	0.011	0.002	0.014
assign-physeq	0.007	0.002	0.009
assign-pred_matrix	0.007	0.002	0.009
assoc_param-methods	0.005	0.002	0.008
association.plot	0.270	0.018	0.291
associations-methods	0.009	0.002	0.011
check.associations	0.011	0.002	0.015
check.confounders	0.452	0.024	0.480
create.data.split	0.021	0.003	0.023
create.label	0.002	0.002	0.004
data_split-methods	0.005	0.002	0.007
eval_data-methods	0.005	0.002	0.007
evaluate.predictions	1.652	0.077	1.745
feature_type-methods	0.005	0.002	0.008
feature_weights-methods	0.036	0.009	0.045
filt_feat-methods	0.007	0.002	0.009
filt_params-methods	0.007	0.002	0.009
filter.features	0.020	0.003	0.023
filter.label	0.011	0.002	0.013
get.filt_feat.matrix	0.006	0.002	0.009
get.norm_feat.matrix	0.007	0.002	0.009
get.orig_feat.matrix	0.007	0.002	0.009
label-methods	0.007	0.002	0.008
make.predictions	26.171	0.392	26.773
meta-methods	0.022	0.003	0.024
model.evaluation.plot	0.026	0.010	0.035
model.interpretation.plot	25.384	0.430	26.169
model_list-methods	0.006	0.002	0.008
model_type-methods	0.006	0.002	0.008
models-methods	0.006	0.002	0.008
norm_feat-methods	0.005	0.002	0.007
norm_params-methods	0.006	0.002	0.008
normalize.features	0.015	0.002	0.017
orig_feat-methods	0.006	0.002	0.008
physeq-methods	0.009	0.002	0.011
pred_matrix-methods	0.006	0.002	0.008
read.label	0.009	0.001	0.009
read.lefse	0.703	0.014	0.721
select.samples	0.051	0.003	0.054
siamcat	1.111	0.018	1.147
siamcat.to.lefse	0.023	0.004	0.027
siamcat.to.maaslin	0.023	0.004	0.027
summarize.features	1.431	0.214	1.674
train.model	24.852	0.412	25.749
validate.data	0.019	0.003	0.021
volcano.plot	0.011	0.004	0.016
weight_matrix-methods	0.006	0.002	0.009