Mac ARM64 build report for BioC 3.18 - CHECK results for SIAMCAT on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4388
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_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SIAMCAT.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.6.0’
* package encoding: UTF-8
* 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  5.1Mb
  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 ... 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
assign-model_list         24.316  0.544  26.140
train.model               23.920  0.667  25.893
model.interpretation.plot 23.594  0.530  25.261
make.predictions          23.571  0.515  25.313
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/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	0.012	0.005	0.017
add.meta.pred	0.032	0.003	0.038
assign-associations	0.010	0.002	0.012
assign-data_split	0.010	0.002	0.011
assign-eval_data	0.009	0.002	0.012
assign-filt_feat	0.007	0.001	0.009
assign-label	0.009	0.002	0.013
assign-meta	0.047	0.002	0.054
assign-model_list	24.316	0.544	26.140
assign-norm_feat	0.009	0.002	0.012
assign-orig_feat	0.014	0.002	0.016
assign-physeq	0.010	0.002	0.013
assign-pred_matrix	0.009	0.002	0.012
assoc_param-methods	0.008	0.002	0.010
association.plot	0.249	0.016	0.266
associations-methods	0.012	0.002	0.015
check.associations	0.014	0.002	0.016
check.confounders	0.516	0.024	0.551
create.data.split	0.024	0.002	0.026
create.label	0.004	0.003	0.006
data_split-methods	0.008	0.002	0.011
eval_data-methods	0.009	0.002	0.011
evaluate.predictions	1.671	0.097	1.862
feature_type-methods	0.009	0.002	0.011
feature_weights-methods	0.009	0.002	0.010
filt_feat-methods	0.009	0.002	0.011
filt_params-methods	0.008	0.002	0.011
filter.features	0.018	0.003	0.023
filter.label	0.011	0.003	0.020
get.filt_feat.matrix	0.009	0.002	0.011
get.norm_feat.matrix	0.008	0.002	0.010
get.orig_feat.matrix	0.008	0.003	0.012
label-methods	0.008	0.002	0.010
make.predictions	23.571	0.515	25.313
meta-methods	0.026	0.003	0.030
model.evaluation.plot	0.027	0.008	0.037
model.interpretation.plot	23.594	0.530	25.261
model_list-methods	0.009	0.003	0.012
model_type-methods	0.008	0.003	0.012
models-methods	0.007	0.002	0.011
norm_feat-methods	0.008	0.003	0.010
norm_params-methods	0.008	0.003	0.012
normalize.features	0.017	0.003	0.020
orig_feat-methods	0.009	0.002	0.011
physeq-methods	0.011	0.002	0.015
pred_matrix-methods	0.009	0.002	0.011
read.label	0.009	0.002	0.014
read.lefse	0.622	0.033	0.690
select.samples	0.057	0.004	0.061
siamcat	0.348	0.023	0.391
siamcat.to.lefse	0.028	0.003	0.033
siamcat.to.maaslin	0.029	0.005	0.038
summarize.features	2.006	0.377	2.525
train.model	23.920	0.667	25.893
validate.data	0.021	0.003	0.024
volcano.plot	0.015	0.004	0.020
weight_matrix-methods	0.008	0.002	0.010

CHECK results for SIAMCAT on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings