Multiple platform build/check report for BioC 3.13 - CHECK results for SIAMCAT on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .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  5.4Mb
  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 ... NOTE
  Note: found 10 marked UTF-8 strings
* 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 25.295  0.146  25.467
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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	0.068	0.011	0.078
add.meta.pred	0.096	0.004	0.099
assign-associations	0.502	0.003	0.505
assign-data_split	0.029	0.005	0.034
assign-eval_data	0.021	0.003	0.023
assign-filt_feat	0.022	0.002	0.024
assign-label	0.025	0.003	0.028
assign-meta	0.063	0.006	0.069
assign-model_list	0.025	0.002	0.026
assign-norm_feat	0.022	0.002	0.024
assign-orig_feat	0.035	0.004	0.039
assign-physeq	0.022	0.002	0.024
assign-pred_matrix	0.040	0.004	0.044
assoc_param-methods	0.022	0.002	0.025
associations-methods	0.024	0.002	0.026
check.associations	0.300	0.019	0.323
check.confounders	0.692	0.039	0.732
create.data.split	0.057	0.003	0.060
create.label	0.006	0.002	0.008
data_split-methods	0.025	0.002	0.027
eval_data-methods	0.031	0.003	0.034
evaluate.predictions	2.951	0.066	3.019
feature_type-methods	0.017	0.002	0.019
feature_weights-methods	0.023	0.003	0.026
filt_feat-methods	0.034	0.004	0.038
filt_params-methods	0.023	0.003	0.025
filter.features	0.034	0.003	0.037
filter.label	0.022	0.001	0.023
get.filt_feat.matrix	0.031	0.002	0.034
get.norm_feat.matrix	0.019	0.002	0.021
get.orig_feat.matrix	0.026	0.003	0.029
label-methods	0.030	0.003	0.034
make.predictions	0.189	0.003	0.193
meta-methods	0.053	0.005	0.059
model.evaluation.plot	0.042	0.006	0.049
model.interpretation.plot	0.092	0.007	0.100
model_list-methods	0.025	0.003	0.027
model_type-methods	0.034	0.003	0.037
models-methods	0.022	0.002	0.024
norm_feat-methods	0.023	0.003	0.025
norm_params-methods	0.027	0.004	0.031
normalize.features	0.058	0.004	0.063
orig_feat-methods	0.021	0.002	0.022
physeq-methods	0.031	0.002	0.033
pred_matrix-methods	0.027	0.003	0.030
read.label	0.017	0.000	0.018
read.lefse	1.403	0.028	1.431
select.samples	0.075	0.002	0.078
siamcat	0.241	0.011	0.253
siamcat.to.lefse	0.056	0.006	0.062
siamcat.to.maaslin	0.036	0.003	0.039
summarize.features	2.055	0.196	2.253
train.model	25.295	0.146	25.467
validate.data	0.049	0.002	0.051
weight_matrix-methods	0.020	0.002	0.022

CHECK results for SIAMCAT on machv2

Summary

Command output

Installation output

Tests output

Example timings