Mac ARM64 build report for BioC 3.17 - CHECK results for SIAMCAT on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4346
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*

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### Running command:
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###   /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_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SIAMCAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'tune(method = "grid_search", ': unused argument (resolution = grid.size) 
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SIAMCAT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 R 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 ... NOTE
train.model: possible error in tune(method = "grid_search", task =
  task, learner = lrn.fold, resampling = rsmp("cv", folds = 5),
  measures = msr(measure), resolution = grid.size): unused argument
  (resolution = grid.size)
* 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         27.385  0.825  52.312
make.predictions          27.150  0.716  49.803
train.model               26.728  0.682  50.743
model.interpretation.plot 26.322  0.714  50.022
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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
Note: possible error in 'tune(method = "grid_search", ': unused argument (resolution = grid.size) 
** 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

name	user	system	elapsed
accessSlot	0.009	0.003	0.021
add.meta.pred	0.033	0.003	0.066
assign-associations	0.007	0.002	0.014
assign-data_split	0.007	0.001	0.016
assign-eval_data	0.007	0.002	0.017
assign-filt_feat	0.007	0.002	0.018
assign-label	0.007	0.002	0.023
assign-meta	0.032	0.002	0.067
assign-model_list	27.385	0.825	52.312
assign-norm_feat	0.007	0.001	0.016
assign-orig_feat	0.012	0.001	0.026
assign-physeq	0.007	0.001	0.016
assign-pred_matrix	0.007	0.002	0.015
assoc_param-methods	0.005	0.001	0.012
association.plot	0.281	0.020	0.535
associations-methods	0.010	0.002	0.022
check.associations	2.291	0.033	4.270
check.confounders	0.511	0.025	0.994
create.data.split	0.024	0.002	0.050
create.label	0.002	0.001	0.008
data_split-methods	0.005	0.001	0.014
eval_data-methods	0.006	0.001	0.015
evaluate.predictions	0.023	0.002	0.046
feature_type-methods	0.006	0.002	0.015
feature_weights-methods	0.006	0.002	0.014
filt_feat-methods	0.006	0.001	0.013
filt_params-methods	0.005	0.001	0.011
filter.features	0.045	0.003	0.089
filter.label	0.009	0.001	0.020
get.filt_feat.matrix	0.007	0.001	0.016
get.norm_feat.matrix	0.006	0.002	0.015
get.orig_feat.matrix	0.006	0.002	0.018
label-methods	0.006	0.002	0.016
make.predictions	27.150	0.716	49.803
meta-methods	0.023	0.002	0.037
model.evaluation.plot	0.028	0.010	0.064
model.interpretation.plot	26.322	0.714	50.022
model_list-methods	0.006	0.002	0.016
model_type-methods	0.006	0.002	0.016
models-methods	0.006	0.001	0.012
norm_feat-methods	0.006	0.001	0.013
norm_params-methods	0.006	0.001	0.016
normalize.features	0.016	0.001	0.036
orig_feat-methods	0.007	0.001	0.016
physeq-methods	0.033	0.002	0.068
pred_matrix-methods	0.007	0.001	0.022
read.label	0.014	0.001	0.034
read.lefse	1.167	0.036	2.238
select.samples	0.064	0.002	0.125
siamcat	0.242	0.006	0.502
siamcat.to.lefse	0.024	0.002	0.048
siamcat.to.maaslin	0.024	0.003	0.043
summarize.features	1.670	0.082	3.237
train.model	26.728	0.682	50.743
validate.data	0.023	0.002	0.047
volcano.plot	0.013	0.003	0.029
weight_matrix-methods	0.006	0.001	0.011

CHECK results for SIAMCAT on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings