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"	4741
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4483
merida1	macOS 12.7.4 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4512
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
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: 2024-07-11 11:48:21 -0400 (Thu, 11 Jul 2024)

EndedAt: 2024-07-11 11:59:50 -0400 (Thu, 11 Jul 2024)

EllapsedTime: 688.8 seconds

RetCode: 0

Status: OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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 12.7.5
* 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               47.582  0.657  56.285
model.interpretation.plot 46.793  0.641  55.433
assign-model_list         44.535  0.817  49.791
make.predictions          42.612  0.454  47.480
evaluate.predictions       4.643  0.140   5.583
* 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

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


* 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	0.011	0.034
add.meta.pred	0.551	0.007	0.569
assign-associations	0.012	0.003	0.015
assign-data_split	0.012	0.003	0.017
assign-eval_data	0.011	0.004	0.015
assign-filt_feat	0.012	0.004	0.024
assign-label	0.013	0.003	0.022
assign-meta	0.059	0.004	0.078
assign-model_list	44.535	0.817	49.791
assign-norm_feat	0.011	0.003	0.015
assign-orig_feat	0.019	0.003	0.021
assign-physeq	0.013	0.004	0.016
assign-pred_matrix	0.011	0.002	0.013
assoc_param-methods	0.006	0.002	0.009
association.plot	0.398	0.024	1.188
associations-methods	0.034	0.005	0.044
check.associations	0.019	0.003	0.026
check.confounders	1.019	0.038	1.279
create.data.split	0.048	0.004	0.064
create.label	0.005	0.003	0.007
data_split-methods	0.008	0.002	0.011
eval_data-methods	0.009	0.003	0.013
evaluate.predictions	4.643	0.140	5.583
feature_type-methods	0.009	0.003	0.013
feature_weights-methods	0.008	0.002	0.013
filt_feat-methods	0.009	0.002	0.015
filt_params-methods	0.008	0.003	0.012
filter.features	0.064	0.008	0.087
filter.label	0.013	0.002	0.019
get.filt_feat.matrix	0.008	0.003	0.013
get.norm_feat.matrix	0.010	0.002	0.014
get.orig_feat.matrix	0.009	0.003	0.014
label-methods	0.009	0.003	0.013
make.predictions	42.612	0.454	47.480
meta-methods	0.033	0.004	0.045
model.evaluation.plot	0.066	0.013	0.093
model.interpretation.plot	46.793	0.641	55.433
model_list-methods	0.009	0.003	0.014
model_type-methods	0.009	0.003	0.014
models-methods	0.008	0.002	0.016
norm_feat-methods	0.009	0.003	0.012
norm_params-methods	0.009	0.003	0.013
normalize.features	0.027	0.003	0.039
orig_feat-methods	0.009	0.003	0.015
physeq-methods	0.016	0.003	0.025
pred_matrix-methods	0.009	0.003	0.016
read.label	0.018	0.002	0.027
read.lefse	1.555	0.058	2.000
select.samples	0.143	0.004	0.179
siamcat	1.168	0.025	1.382
siamcat.to.lefse	0.035	0.004	0.049
siamcat.to.maaslin	0.038	0.004	0.046
summarize.features	3.285	0.158	3.998
train.model	47.582	0.657	56.285
validate.data	0.041	0.003	0.048
volcano.plot	0.023	0.006	0.031
weight_matrix-methods	0.009	0.002	0.013