Multiple platform build/check report for BioC 3.15 - CHECK results for SIAMCAT on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
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_2.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.0.1’
* 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 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 ... 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               42.687  0.422  43.156
assign-model_list         41.945  0.603  42.604
make.predictions          41.810  0.375  42.255
model.interpretation.plot 41.325  0.427  41.796
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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

name	user	system	elapsed
accessSlot	0.015	0.004	0.018
add.meta.pred	0.102	0.003	0.106
assign-associations	0.013	0.002	0.016
assign-data_split	0.014	0.002	0.016
assign-eval_data	0.013	0.002	0.016
assign-filt_feat	0.013	0.003	0.016
assign-label	0.013	0.002	0.015
assign-meta	0.053	0.002	0.055
assign-model_list	41.945	0.603	42.604
assign-norm_feat	0.013	0.001	0.015
assign-orig_feat	0.021	0.002	0.023
assign-physeq	0.014	0.001	0.015
assign-pred_matrix	0.070	0.008	0.079
assoc_param-methods	0.010	0.001	0.011
association.plot	0.374	0.013	0.388
associations-methods	0.016	0.002	0.019
check.associations	3.862	0.014	3.881
check.confounders	0.829	0.021	0.851
create.data.split	0.039	0.002	0.041
create.label	0.004	0.001	0.006
data_split-methods	0.010	0.002	0.013
eval_data-methods	0.011	0.003	0.013
evaluate.predictions	0.040	0.002	0.042
feature_type-methods	0.010	0.002	0.012
feature_weights-methods	0.010	0.003	0.012
filt_feat-methods	0.010	0.001	0.011
filt_params-methods	0.009	0.002	0.011
filter.features	0.027	0.001	0.029
filter.label	0.011	0.002	0.014
get.filt_feat.matrix	0.035	0.003	0.037
get.norm_feat.matrix	0.011	0.001	0.013
get.orig_feat.matrix	0.011	0.002	0.013
label-methods	0.011	0.002	0.013
make.predictions	41.810	0.375	42.255
meta-methods	0.034	0.002	0.037
model.evaluation.plot	0.040	0.006	0.047
model.interpretation.plot	41.325	0.427	41.796
model_list-methods	0.010	0.001	0.011
model_type-methods	0.010	0.001	0.011
models-methods	0.010	0.002	0.011
norm_feat-methods	0.010	0.002	0.012
norm_params-methods	0.009	0.002	0.011
normalize.features	0.027	0.002	0.029
orig_feat-methods	0.011	0.001	0.012
physeq-methods	0.016	0.001	0.018
pred_matrix-methods	0.010	0.001	0.012
read.label	0.017	0.001	0.018
read.lefse	1.262	0.019	1.282
select.samples	0.115	0.002	0.118
siamcat	0.428	0.018	0.447
siamcat.to.lefse	0.036	0.002	0.038
siamcat.to.maaslin	0.041	0.002	0.043
summarize.features	2.756	0.255	3.014
train.model	42.687	0.422	43.156
validate.data	0.035	0.002	0.036
volcano.plot	0.019	0.002	0.020
weight_matrix-methods	0.009	0.002	0.010

CHECK results for SIAMCAT on merida1

Summary

Command output

Installation output

Tests output

Example timings