Multiple platform build/check report for BioC 3.18 - CHECK results for SIAMCAT on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4676
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4414
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4437
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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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SIAMCAT_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.6.0’
* 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 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 loading without being on the library search path ... 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
model.interpretation.plot 19.415  0.156  19.571
assign-model_list         18.962  0.393  19.355
make.predictions          19.124  0.220  19.345
train.model               18.914  0.148  19.062
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SIAMCAT_confounder.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_holdout.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_meta.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_ml_pitfalls.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_read-in.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_vignette.Rmd’ using ‘ASCII’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SIAMCAT
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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	0.008	0.000	0.009
add.meta.pred	0.027	0.000	0.027
assign-associations	0.008	0.000	0.007
assign-data_split	0.007	0.000	0.008
assign-eval_data	0.007	0.000	0.007
assign-filt_feat	0.007	0.000	0.007
assign-label	0.007	0.000	0.007
assign-meta	0.022	0.003	0.026
assign-model_list	18.962	0.393	19.355
assign-norm_feat	0.007	0.000	0.007
assign-orig_feat	0.011	0.000	0.011
assign-physeq	0.007	0.000	0.007
assign-pred_matrix	0.007	0.000	0.007
assoc_param-methods	0.006	0.000	0.005
association.plot	0.207	0.003	0.210
associations-methods	0.009	0.001	0.008
check.associations	0.01	0.00	0.01
check.confounders	0.430	0.003	0.434
create.data.split	0.017	0.004	0.021
create.label	0.002	0.001	0.002
data_split-methods	0.006	0.000	0.005
eval_data-methods	0.002	0.003	0.006
evaluate.predictions	1.531	0.008	1.539
feature_type-methods	0.006	0.000	0.006
feature_weights-methods	0.006	0.001	0.005
filt_feat-methods	0.002	0.003	0.005
filt_params-methods	0.005	0.000	0.006
filter.features	0.009	0.004	0.013
filter.label	0.007	0.000	0.007
get.filt_feat.matrix	0.006	0.000	0.005
get.norm_feat.matrix	0.019	0.000	0.019
get.orig_feat.matrix	0.006	0.000	0.006
label-methods	0.006	0.000	0.006
make.predictions	19.124	0.220	19.345
meta-methods	0.011	0.007	0.019
model.evaluation.plot	0.023	0.001	0.023
model.interpretation.plot	19.415	0.156	19.571
model_list-methods	0.006	0.000	0.006
model_type-methods	0.006	0.000	0.006
models-methods	0.005	0.000	0.006
norm_feat-methods	0.005	0.000	0.006
norm_params-methods	0.005	0.000	0.005
normalize.features	0.014	0.000	0.014
orig_feat-methods	0.006	0.000	0.006
physeq-methods	0.009	0.000	0.010
pred_matrix-methods	0.006	0.000	0.006
read.label	0.007	0.000	0.007
read.lefse	0.549	0.031	0.581
select.samples	0.055	0.000	0.055
siamcat	0.287	0.008	0.295
siamcat.to.lefse	0.018	0.004	0.022
siamcat.to.maaslin	0.020	0.004	0.024
summarize.features	2.058	0.088	2.146
train.model	18.914	0.148	19.062
validate.data	0.018	0.000	0.018
volcano.plot	0.011	0.000	0.011
weight_matrix-methods	0.005	0.000	0.005

CHECK results for SIAMCAT on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings