Multiple platform build/check report for BioC 3.17 - CHECK results for SIAMCAT on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4626
palomino3	Windows Server 2022 Datacenter	x64	4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"	4379
merida1	macOS 12.6.4 Monterey	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4395
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/meat/SIAMCAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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/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         43.972  0.863  56.971
make.predictions          43.952  0.730  57.227
train.model               43.517  0.663  56.913
model.interpretation.plot 43.488  0.664  56.211
summarize.features         4.910  0.188   6.700
check.associations         3.569  0.040   5.104
* 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/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-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
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	0.014	0.011	0.046
add.meta.pred	0.055	0.010	0.102
assign-associations	0.013	0.004	0.041
assign-data_split	0.013	0.003	0.023
assign-eval_data	0.012	0.004	0.027
assign-filt_feat	0.013	0.004	0.025
assign-label	0.035	0.004	0.049
assign-meta	0.055	0.004	0.095
assign-model_list	43.972	0.863	56.971
assign-norm_feat	0.012	0.002	0.020
assign-orig_feat	0.021	0.003	0.032
assign-physeq	0.013	0.003	0.021
assign-pred_matrix	0.012	0.003	0.019
assoc_param-methods	0.009	0.003	0.015
association.plot	0.426	0.025	0.625
associations-methods	0.016	0.004	0.028
check.associations	3.569	0.040	5.104
check.confounders	0.918	0.037	1.245
create.data.split	0.048	0.003	0.069
create.label	0.004	0.002	0.007
data_split-methods	0.009	0.003	0.015
eval_data-methods	0.010	0.003	0.015
evaluate.predictions	0.051	0.006	0.079
feature_type-methods	0.009	0.003	0.019
feature_weights-methods	0.036	0.003	0.055
filt_feat-methods	0.010	0.002	0.015
filt_params-methods	0.009	0.003	0.015
filter.features	0.030	0.004	0.042
filter.label	0.012	0.003	0.018
get.filt_feat.matrix	0.009	0.003	0.014
get.norm_feat.matrix	0.009	0.003	0.015
get.orig_feat.matrix	0.010	0.003	0.018
label-methods	0.009	0.003	0.017
make.predictions	43.952	0.730	57.227
meta-methods	0.034	0.004	0.051
model.evaluation.plot	0.041	0.012	0.074
model.interpretation.plot	43.488	0.664	56.211
model_list-methods	0.010	0.003	0.016
model_type-methods	0.009	0.003	0.026
models-methods	0.009	0.003	0.015
norm_feat-methods	0.009	0.003	0.013
norm_params-methods	0.009	0.003	0.019
normalize.features	0.049	0.004	0.064
orig_feat-methods	0.010	0.002	0.018
physeq-methods	0.018	0.003	0.026
pred_matrix-methods	0.010	0.003	0.017
read.label	0.021	0.002	0.024
read.lefse	1.469	0.049	1.915
select.samples	0.126	0.004	0.159
siamcat	0.406	0.020	0.541
siamcat.to.lefse	0.040	0.004	0.055
siamcat.to.maaslin	0.041	0.004	0.053
summarize.features	4.910	0.188	6.700
train.model	43.517	0.663	56.913
validate.data	0.036	0.003	0.051
volcano.plot	0.021	0.005	0.031
weight_matrix-methods	0.008	0.003	0.018

CHECK results for SIAMCAT on merida1

Summary

Command output

Installation output

Tests output

Example timings