Multiple platform build/check report for BioC 3.19 - CHECK results for SIAMCAT on kjohnson1

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
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4529
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4479
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: 2.8.0

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: 2024-10-15 11:55:39 -0400 (Tue, 15 Oct 2024)

EndedAt: 2024-10-15 12:01:34 -0400 (Tue, 15 Oct 2024)

EllapsedTime: 354.7 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_2.8.0.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: 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 13.6.6
* 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
assign-model_list         26.970  0.777  29.058
make.predictions          26.622  0.480  28.899
train.model               26.243  0.658  28.887
model.interpretation.plot 26.186  0.566  28.086
* 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
###
##############################################################################
##############################################################################


* 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	0.010	0.004	0.014
add.meta.pred	0.031	0.003	0.039
assign-associations	0.009	0.003	0.012
assign-data_split	0.009	0.003	0.011
assign-eval_data	0.008	0.002	0.011
assign-filt_feat	0.146	0.003	0.152
assign-label	0.010	0.002	0.013
assign-meta	0.028	0.003	0.033
assign-model_list	26.970	0.777	29.058
assign-norm_feat	0.009	0.003	0.012
assign-orig_feat	0.012	0.003	0.014
assign-physeq	0.008	0.003	0.011
assign-pred_matrix	0.008	0.002	0.010
assoc_param-methods	0.007	0.002	0.009
association.plot	0.274	0.017	0.305
associations-methods	0.012	0.003	0.015
check.associations	0.012	0.002	0.014
check.confounders	0.473	0.029	0.525
create.data.split	0.023	0.003	0.024
create.label	0.003	0.002	0.005
data_split-methods	0.007	0.002	0.010
eval_data-methods	0.007	0.003	0.010
evaluate.predictions	1.740	0.092	1.931
feature_type-methods	0.007	0.002	0.010
feature_weights-methods	0.007	0.002	0.009
filt_feat-methods	0.007	0.002	0.009
filt_params-methods	0.007	0.002	0.009
filter.features	0.016	0.002	0.017
filter.label	0.009	0.002	0.011
get.filt_feat.matrix	0.007	0.002	0.009
get.norm_feat.matrix	0.008	0.002	0.010
get.orig_feat.matrix	0.007	0.002	0.010
label-methods	0.007	0.002	0.009
make.predictions	26.622	0.480	28.899
meta-methods	0.027	0.003	0.032
model.evaluation.plot	0.030	0.010	0.047
model.interpretation.plot	26.186	0.566	28.086
model_list-methods	0.007	0.002	0.010
model_type-methods	0.006	0.003	0.010
models-methods	0.007	0.003	0.009
norm_feat-methods	0.007	0.002	0.010
norm_params-methods	0.007	0.002	0.008
normalize.features	0.015	0.002	0.018
orig_feat-methods	0.007	0.002	0.010
physeq-methods	0.012	0.002	0.016
pred_matrix-methods	0.008	0.002	0.010
read.label	0.009	0.001	0.010
read.lefse	0.730	0.017	0.769
select.samples	0.061	0.003	0.067
siamcat	0.373	0.013	0.393
siamcat.to.lefse	0.029	0.003	0.033
siamcat.to.maaslin	0.029	0.002	0.033
summarize.features	2.359	0.176	2.654
train.model	26.243	0.658	28.887
validate.data	0.018	0.002	0.023
volcano.plot	0.009	0.004	0.014
weight_matrix-methods	0.004	0.002	0.006