Multiple platform build/check report for BioC 3.18 - CHECK results for SIAMCAT on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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/meat/SIAMCAT.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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         24.246  0.621  25.100
make.predictions          24.119  0.515  24.834
train.model               23.300  0.482  23.908
model.interpretation.plot 22.968  0.519  23.621
* 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/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-x86_64/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	0.008	0.005	0.013
add.meta.pred	0.029	0.003	0.032
assign-associations	0.007	0.002	0.009
assign-data_split	0.008	0.001	0.010
assign-eval_data	0.006	0.002	0.008
assign-filt_feat	0.008	0.001	0.009
assign-label	0.008	0.002	0.010
assign-meta	0.050	0.004	0.055
assign-model_list	24.246	0.621	25.100
assign-norm_feat	0.006	0.001	0.008
assign-orig_feat	0.014	0.002	0.015
assign-physeq	0.008	0.002	0.011
assign-pred_matrix	0.006	0.002	0.008
assoc_param-methods	0.007	0.003	0.009
association.plot	0.229	0.017	0.249
associations-methods	0.008	0.002	0.011
check.associations	0.010	0.002	0.012
check.confounders	0.507	0.026	0.540
create.data.split	0.026	0.002	0.028
create.label	0.003	0.001	0.003
data_split-methods	0.005	0.001	0.006
eval_data-methods	0.005	0.002	0.006
evaluate.predictions	1.869	0.076	1.958
feature_type-methods	0.031	0.006	0.039
feature_weights-methods	0.006	0.002	0.009
filt_feat-methods	0.006	0.001	0.006
filt_params-methods	0.006	0.001	0.008
filter.features	0.020	0.002	0.022
filter.label	0.007	0.001	0.009
get.filt_feat.matrix	0.006	0.001	0.007
get.norm_feat.matrix	0.006	0.001	0.009
get.orig_feat.matrix	0.007	0.002	0.009
label-methods	0.006	0.002	0.008
make.predictions	24.119	0.515	24.834
meta-methods	0.038	0.003	0.042
model.evaluation.plot	0.026	0.009	0.036
model.interpretation.plot	22.968	0.519	23.621
model_list-methods	0.007	0.002	0.009
model_type-methods	0.006	0.002	0.008
models-methods	0.007	0.002	0.009
norm_feat-methods	0.023	0.002	0.025
norm_params-methods	0.008	0.001	0.008
normalize.features	0.020	0.001	0.021
orig_feat-methods	0.007	0.002	0.009
physeq-methods	0.009	0.001	0.010
pred_matrix-methods	0.007	0.002	0.008
read.label	0.009	0.001	0.010
read.lefse	0.651	0.016	0.669
select.samples	0.076	0.002	0.079
siamcat	0.344	0.019	0.365
siamcat.to.lefse	0.026	0.003	0.029
siamcat.to.maaslin	0.025	0.002	0.027
summarize.features	2.479	0.310	2.805
train.model	23.300	0.482	23.908
validate.data	0.025	0.003	0.027
volcano.plot	0.013	0.003	0.016
weight_matrix-methods	0.006	0.001	0.008

CHECK results for SIAMCAT on lconway

Summary

Command output

Installation output

Tests output

Example timings