Multiple platform build/check report for BioC 3.19 - CHECK results for SIAMCAT on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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 merida1

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: 2.8.0

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_2.8.0.tar.gz

StartedAt: 2024-10-17 13:09:51 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 13:20:34 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 643.3 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.8.0’
* 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
train.model               47.394  0.643  57.591
assign-model_list         47.117  0.869  55.454
make.predictions          46.305  0.549  52.125
model.interpretation.plot 43.099  0.581  48.082
summarize.features         4.748  0.154   6.436
evaluate.predictions       4.375  0.170   5.154
* 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-3.19-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
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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	0.014	0.010	0.027
add.meta.pred	0.051	0.004	0.060
assign-associations	0.012	0.003	0.017
assign-data_split	0.012	0.003	0.019
assign-eval_data	0.012	0.003	0.017
assign-filt_feat	0.123	0.004	0.144
assign-label	0.013	0.003	0.018
assign-meta	0.056	0.003	0.075
assign-model_list	47.117	0.869	55.454
assign-norm_feat	0.011	0.003	0.018
assign-orig_feat	0.021	0.004	0.028
assign-physeq	0.012	0.003	0.015
assign-pred_matrix	0.011	0.002	0.014
assoc_param-methods	0.009	0.004	0.012
association.plot	0.423	0.025	0.634
associations-methods	0.014	0.004	0.018
check.associations	0.017	0.004	0.021
check.confounders	0.951	0.042	1.286
create.data.split	0.049	0.004	0.057
create.label	0.004	0.002	0.006
data_split-methods	0.009	0.002	0.011
eval_data-methods	0.009	0.003	0.013
evaluate.predictions	4.375	0.170	5.154
feature_type-methods	0.010	0.002	0.012
feature_weights-methods	0.009	0.003	0.014
filt_feat-methods	0.009	0.002	0.012
filt_params-methods	0.008	0.003	0.011
filter.features	0.028	0.004	0.033
filter.label	0.012	0.002	0.015
get.filt_feat.matrix	0.008	0.003	0.012
get.norm_feat.matrix	0.009	0.004	0.012
get.orig_feat.matrix	0.009	0.004	0.012
label-methods	0.009	0.004	0.013
make.predictions	46.305	0.549	52.125
meta-methods	0.034	0.004	0.047
model.evaluation.plot	0.043	0.013	1.387
model.interpretation.plot	43.099	0.581	48.082
model_list-methods	0.009	0.003	0.014
model_type-methods	0.009	0.003	0.015
models-methods	0.008	0.003	0.017
norm_feat-methods	0.008	0.002	0.012
norm_params-methods	0.009	0.003	0.013
normalize.features	0.026	0.003	0.038
orig_feat-methods	0.009	0.002	0.017
physeq-methods	0.016	0.003	0.023
pred_matrix-methods	0.009	0.004	0.014
read.label	0.017	0.003	0.027
read.lefse	1.511	0.026	2.009
select.samples	0.136	0.005	0.190
siamcat	0.484	0.019	0.670
siamcat.to.lefse	0.039	0.005	0.061
siamcat.to.maaslin	0.043	0.005	0.061
summarize.features	4.748	0.154	6.436
train.model	47.394	0.643	57.591
validate.data	0.038	0.004	0.046
volcano.plot	0.021	0.005	0.030
weight_matrix-methods	0.008	0.003	0.013