Multiple platform build/check report for BioC 3.14 - CHECK results for SIAMCAT on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.14.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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 27.458  0.127  27.612
* 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-3.14-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/4.1/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	0.046	0.009	0.055
add.meta.pred	0.123	0.004	0.128
assign-associations	0.033	0.004	0.038
assign-data_split	0.490	0.005	0.494
assign-eval_data	0.028	0.002	0.030
assign-filt_feat	0.026	0.004	0.031
assign-label	0.031	0.003	0.034
assign-meta	0.066	0.002	0.068
assign-model_list	0.044	0.008	0.052
assign-norm_feat	0.031	0.004	0.035
assign-orig_feat	0.036	0.002	0.038
assign-physeq	0.030	0.003	0.033
assign-pred_matrix	0.026	0.001	0.027
assoc_param-methods	0.033	0.007	0.040
associations-methods	0.028	0.003	0.031
check.associations	0.370	0.022	0.393
check.confounders	0.742	0.041	0.824
create.data.split	0.063	0.003	0.066
create.label	0.006	0.001	0.008
data_split-methods	0.058	0.005	0.064
eval_data-methods	0.029	0.002	0.031
evaluate.predictions	0.067	0.006	0.074
feature_type-methods	0.030	0.002	0.032
feature_weights-methods	0.055	0.007	0.063
filt_feat-methods	0.029	0.003	0.033
filt_params-methods	0.030	0.003	0.033
filter.features	0.038	0.002	0.041
filter.label	0.039	0.003	0.042
get.filt_feat.matrix	0.026	0.002	0.027
get.norm_feat.matrix	0.022	0.003	0.024
get.orig_feat.matrix	0.036	0.004	0.040
label-methods	0.024	0.002	0.024
make.predictions	0.259	0.005	0.264
meta-methods	0.050	0.002	0.052
model.evaluation.plot	0.044	0.005	0.050
model.interpretation.plot	0.111	0.007	0.118
model_list-methods	0.035	0.003	0.038
model_type-methods	0.027	0.002	0.029
models-methods	0.026	0.003	0.029
norm_feat-methods	0.027	0.004	0.030
norm_params-methods	0.044	0.005	0.049
normalize.features	0.044	0.002	0.046
orig_feat-methods	0.028	0.002	0.030
physeq-methods	0.027	0.001	0.028
pred_matrix-methods	0.040	0.003	0.043
read.label	0.013	0.001	0.014
read.lefse	1.576	0.065	1.642
select.samples	0.111	0.004	0.114
siamcat	0.319	0.016	0.380
siamcat.to.lefse	0.087	0.007	0.094
siamcat.to.maaslin	0.052	0.003	0.056
summarize.features	3.108	0.413	3.523
train.model	27.458	0.127	27.612
validate.data	0.077	0.004	0.082
weight_matrix-methods	0.034	0.003	0.037

CHECK results for SIAMCAT on machv2

Summary

Command output

Installation output

Tests output

Example timings