Mac ARM64 build report for BioC 3.20 - CHECK results for SIAMCAT on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4381
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_2.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SIAMCAT.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.9.0’
* 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 code 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 24.222  0.339  24.702
make.predictions          24.031  0.333  24.466
train.model               23.552  0.449  24.100
assign-model_list         23.390  0.423  23.935
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-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/4.4-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	0.010	0.005	0.014
add.meta.pred	0.581	0.004	0.588
assign-associations	0.004	0.002	0.006
assign-data_split	0.008	0.002	0.011
assign-eval_data	0.008	0.002	0.010
assign-filt_feat	0.008	0.001	0.010
assign-label	0.008	0.002	0.011
assign-meta	0.019	0.003	0.023
assign-model_list	23.390	0.423	23.935
assign-norm_feat	0.008	0.002	0.010
assign-orig_feat	0.013	0.002	0.016
assign-physeq	0.008	0.002	0.010
assign-pred_matrix	0.023	0.002	0.026
assoc_param-methods	0.007	0.002	0.010
association.plot	0.249	0.017	0.272
associations-methods	0.011	0.002	0.013
check.associations	0.011	0.002	0.014
check.confounders	0.456	0.024	0.483
create.data.split	0.054	0.004	0.058
create.label	0.003	0.002	0.004
data_split-methods	0.007	0.002	0.009
eval_data-methods	0.007	0.002	0.009
evaluate.predictions	1.564	0.063	1.632
feature_type-methods	0.007	0.002	0.008
feature_weights-methods	0.007	0.002	0.009
filt_feat-methods	0.007	0.002	0.009
filt_params-methods	0.007	0.002	0.009
filter.features	0.014	0.003	0.017
filter.label	0.009	0.002	0.012
get.filt_feat.matrix	0.007	0.002	0.009
get.norm_feat.matrix	0.007	0.002	0.009
get.orig_feat.matrix	0.100	0.012	0.112
label-methods	0.009	0.002	0.013
make.predictions	24.031	0.333	24.466
meta-methods	0.025	0.003	0.028
model.evaluation.plot	0.028	0.008	0.037
model.interpretation.plot	24.222	0.339	24.702
model_list-methods	0.007	0.002	0.009
model_type-methods	0.007	0.003	0.009
models-methods	0.007	0.003	0.010
norm_feat-methods	0.007	0.003	0.009
norm_params-methods	0.007	0.002	0.009
normalize.features	0.014	0.002	0.017
orig_feat-methods	0.007	0.002	0.009
physeq-methods	0.010	0.002	0.014
pred_matrix-methods	0.007	0.002	0.009
read.label	0.008	0.001	0.009
read.lefse	0.619	0.012	0.632
select.samples	0.050	0.003	0.053
siamcat	1.065	0.013	1.080
siamcat.to.lefse	0.023	0.003	0.026
siamcat.to.maaslin	0.024	0.003	0.028
summarize.features	1.164	0.201	1.450
train.model	23.552	0.449	24.100
validate.data	0.024	0.003	0.027
volcano.plot	0.014	0.006	0.019
weight_matrix-methods	0.008	0.002	0.009

CHECK results for SIAMCAT on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings