Multiple platform build/check report for BioC 3.13 - CHECK results for SIAMCAT on nebbiolo1

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘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:
  .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 ... 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 18.568   0.54  19.113
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/bbs-3.13-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	0.044	0.004	0.048
add.meta.pred	0.059	0.008	0.066
assign-associations	0.533	0.000	0.534
assign-data_split	0.016	0.000	0.016
assign-eval_data	0.016	0.000	0.016
assign-filt_feat	0.017	0.000	0.016
assign-label	0.013	0.003	0.017
assign-meta	0.041	0.000	0.040
assign-model_list	0.015	0.000	0.015
assign-norm_feat	0.015	0.000	0.016
assign-orig_feat	0.019	0.000	0.019
assign-physeq	0.015	0.000	0.015
assign-pred_matrix	0.015	0.000	0.015
assoc_param-methods	0.02	0.00	0.02
associations-methods	0.018	0.001	0.018
check.associations	0.217	0.000	0.217
check.confounders	0.387	0.003	0.390
create.data.split	0.030	0.000	0.029
create.label	0.004	0.000	0.003
data_split-methods	0.012	0.004	0.015
eval_data-methods	0.023	0.000	0.023
evaluate.predictions	1.593	0.004	1.598
feature_type-methods	0.012	0.004	0.016
feature_weights-methods	0.017	0.003	0.021
filt_feat-methods	0.026	0.000	0.026
filt_params-methods	0.011	0.004	0.015
filter.features	0.016	0.004	0.021
filter.label	0.018	0.000	0.018
get.filt_feat.matrix	0.022	0.004	0.026
get.norm_feat.matrix	0.011	0.004	0.015
get.orig_feat.matrix	0.011	0.004	0.015
label-methods	0.015	0.000	0.014
make.predictions	0.155	0.004	0.160
meta-methods	0.025	0.004	0.030
model.evaluation.plot	0.041	0.000	0.041
model.interpretation.plot	0.059	0.004	0.063
model_list-methods	0.015	0.000	0.014
model_type-methods	0.039	0.000	0.039
models-methods	0.018	0.000	0.018
norm_feat-methods	0.016	0.000	0.016
norm_params-methods	0.017	0.000	0.017
normalize.features	0.036	0.004	0.040
orig_feat-methods	0.016	0.000	0.016
physeq-methods	0.019	0.000	0.020
pred_matrix-methods	0.033	0.000	0.033
read.label	0.01	0.00	0.01
read.lefse	0.543	0.028	0.574
select.samples	0.597	0.004	0.602
siamcat	0.238	0.000	0.237
siamcat.to.lefse	0.034	0.000	0.033
siamcat.to.maaslin	0.561	0.015	0.577
summarize.features	1.130	0.048	1.179
train.model	18.568	0.540	19.113
validate.data	0.027	0.012	0.040
weight_matrix-methods	0.017	0.000	0.016

CHECK results for SIAMCAT on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings