Multiple platform build/check report for BioC 3.15 - CHECK results for SIAMCAT on nebbiolo1

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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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SIAMCAT_2.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ... 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 ... 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 25.917  0.383  26.302
make.predictions          24.260  0.328  24.588
train.model               23.263  0.378  23.644
assign-model_list         22.607  0.466  23.074
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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	0.007	0.004	0.012
add.meta.pred	0.046	0.003	0.051
assign-associations	0.007	0.001	0.007
assign-data_split	0.007	0.000	0.007
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	0.018	0.008	0.026
assign-model_list	22.607	0.466	23.074
assign-norm_feat	0.007	0.002	0.008
assign-orig_feat	0.013	0.000	0.013
assign-physeq	0.008	0.000	0.008
assign-pred_matrix	0.008	0.000	0.008
assoc_param-methods	0.006	0.000	0.006
association.plot	0.208	0.015	0.223
associations-methods	0.009	0.000	0.010
check.associations	1.817	0.031	1.849
check.confounders	0.407	0.004	0.412
create.data.split	0.019	0.001	0.019
create.label	0.003	0.000	0.002
data_split-methods	0.005	0.000	0.005
eval_data-methods	0.006	0.000	0.006
evaluate.predictions	0.019	0.000	0.019
feature_type-methods	0.005	0.000	0.006
feature_weights-methods	0.005	0.000	0.006
filt_feat-methods	0.005	0.000	0.006
filt_params-methods	0.001	0.003	0.005
filter.features	0.013	0.000	0.013
filter.label	0.003	0.004	0.007
get.filt_feat.matrix	0.005	0.001	0.006
get.norm_feat.matrix	0.002	0.002	0.006
get.orig_feat.matrix	0.021	0.001	0.020
label-methods	0.007	0.000	0.007
make.predictions	24.260	0.328	24.588
meta-methods	0.015	0.007	0.023
model.evaluation.plot	0.026	0.000	0.026
model.interpretation.plot	25.917	0.383	26.302
model_list-methods	0.007	0.000	0.006
model_type-methods	0.003	0.004	0.006
models-methods	0.007	0.000	0.006
norm_feat-methods	0.006	0.000	0.006
norm_params-methods	0.006	0.000	0.005
normalize.features	0.015	0.000	0.015
orig_feat-methods	0.003	0.003	0.006
physeq-methods	0.009	0.000	0.010
pred_matrix-methods	0.006	0.000	0.007
read.label	0.008	0.000	0.009
read.lefse	0.520	0.020	0.542
select.samples	0.063	0.004	0.067
siamcat	0.295	0.012	0.307
siamcat.to.lefse	0.023	0.000	0.023
siamcat.to.maaslin	0.025	0.000	0.025
summarize.features	1.592	0.048	1.640
train.model	23.263	0.378	23.644
validate.data	0.014	0.004	0.018
volcano.plot	0.008	0.004	0.013
weight_matrix-methods	0.006	0.000	0.006

CHECK results for SIAMCAT on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings