Multiple platform build/check report for BioC 3.11 - CHECK report 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.1’
* 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 ... OK
* 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 ... OK
* 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 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          29.547  0.100  29.670
evaluate.predictions 12.936  0.099  13.046
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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
** 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	0.046	0.011	0.057
add.meta.pred	0.129	0.003	0.133
assign-associations	0.028	0.002	0.031
assign-data_split	0.029	0.003	0.031
assign-eval_data	0.040	0.004	0.044
assign-filt_feat	0.030	0.005	0.035
assign-label	0.031	0.004	0.035
assign-meta	0.056	0.003	0.059
assign-model_list	0.025	0.003	0.027
assign-norm_feat	0.109	0.005	0.115
assign-orig_feat	0.037	0.004	0.041
assign-physeq	0.023	0.001	0.025
assign-pred_matrix	0.028	0.002	0.029
assoc_param-methods	0.034	0.003	0.038
associations-methods	0.033	0.004	0.037
check.associations	0.756	0.020	0.779
check.confounders	0.682	0.030	0.715
create.data.split	0.068	0.004	0.072
create.label	0.004	0.002	0.005
data_split-methods	0.024	0.002	0.027
eval_data-methods	0.026	0.004	0.030
evaluate.predictions	12.936	0.099	13.046
feature_type-methods	0.021	0.002	0.022
feature_weights-methods	0.041	0.004	0.045
filt_feat-methods	0.027	0.003	0.030
filt_params-methods	0.039	0.006	0.046
filter.features	0.037	0.003	0.040
filter.label	0.030	0.003	0.033
get.filt_feat.matrix	0.025	0.005	0.031
get.norm_feat.matrix	0.022	0.004	0.026
get.orig_feat.matrix	0.030	0.004	0.034
label-methods	0.020	0.001	0.022
make.predictions	0.253	0.004	0.257
meta-methods	0.047	0.003	0.051
model.evaluation.plot	0.032	0.005	0.037
model.interpretation.plot	0.110	0.006	0.118
model_list-methods	0.019	0.002	0.021
model_type-methods	0.032	0.002	0.033
models-methods	0.022	0.002	0.024
norm_feat-methods	0.025	0.002	0.028
norm_params-methods	0.025	0.002	0.027
normalize.features	0.077	0.012	0.089
orig_feat-methods	0.027	0.002	0.030
physeq-methods	0.025	0.001	0.027
pred_matrix-methods	0.022	0.002	0.023
read.label	0.014	0.001	0.015
read.lefse	1.934	0.029	1.966
select.samples	0.122	0.003	0.124
siamcat	0.355	0.008	0.364
siamcat.to.lefse	0.081	0.009	0.089
siamcat.to.maaslin	0.047	0.003	0.051
summarize.features	2.650	0.173	2.828
train.model	29.547	0.100	29.670
validate.data	0.043	0.002	0.045
weight_matrix-methods	0.026	0.002	0.027

CHECK report for SIAMCAT on machv2

Summary

Command output

Installation output

Tests output

Example timings