Multiple platform build/check report for BioC 3.19 - CHECK results for SIAMCAT on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	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*

CHECK results for SIAMCAT on kjohnson1

To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SIAMCAT

Version: 2.8.0

Command: /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_2.8.0.tar.gz

StartedAt: 2024-06-25 09:16:18 -0400 (Tue, 25 Jun 2024)

EndedAt: 2024-06-25 09:22:19 -0400 (Tue, 25 Jun 2024)

EllapsedTime: 360.8 seconds

RetCode: 0

Status: OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘2.8.0’
* 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
train.model               39.211  0.663  40.122
make.predictions          37.952  0.674  38.913
assign-model_list         36.716  0.705  37.674
model.interpretation.plot 36.568  0.631  37.585
* 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-3.19-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* 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

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

name	user	system	elapsed
accessSlot	0.010	0.004	0.015
add.meta.pred	0.631	0.005	0.640
assign-associations	0.008	0.002	0.011
assign-data_split	0.008	0.002	0.010
assign-eval_data	0.008	0.001	0.010
assign-filt_feat	0.009	0.002	0.011
assign-label	0.009	0.002	0.010
assign-meta	0.027	0.005	0.043
assign-model_list	36.716	0.705	37.674
assign-norm_feat	0.009	0.002	0.010
assign-orig_feat	0.012	0.002	0.014
assign-physeq	0.008	0.002	0.011
assign-pred_matrix	0.009	0.002	0.009
assoc_param-methods	0.007	0.002	0.009
association.plot	0.250	0.016	0.266
associations-methods	0.011	0.002	0.014
check.associations	0.013	0.002	0.015
check.confounders	0.476	0.026	0.504
create.data.split	0.022	0.003	0.024
create.label	0.003	0.002	0.005
data_split-methods	0.007	0.002	0.009
eval_data-methods	0.007	0.002	0.009
evaluate.predictions	1.620	0.064	1.688
feature_type-methods	0.007	0.001	0.009
feature_weights-methods	0.006	0.002	0.009
filt_feat-methods	0.007	0.002	0.009
filt_params-methods	0.006	0.002	0.009
filter.features	0.016	0.003	0.018
filter.label	0.009	0.002	0.011
get.filt_feat.matrix	0.007	0.002	0.009
get.norm_feat.matrix	0.006	0.002	0.009
get.orig_feat.matrix	0.007	0.001	0.009
label-methods	0.007	0.002	0.009
make.predictions	37.952	0.674	38.913
meta-methods	0.027	0.003	0.029
model.evaluation.plot	0.056	0.008	0.064
model.interpretation.plot	36.568	0.631	37.585
model_list-methods	0.007	0.002	0.009
model_type-methods	0.007	0.002	0.009
models-methods	0.007	0.002	0.011
norm_feat-methods	0.007	0.001	0.008
norm_params-methods	0.007	0.002	0.009
normalize.features	0.016	0.003	0.018
orig_feat-methods	0.008	0.002	0.009
physeq-methods	0.010	0.002	0.012
pred_matrix-methods	0.007	0.002	0.010
read.label	0.009	0.002	0.010
read.lefse	0.688	0.014	0.703
select.samples	0.054	0.003	0.057
siamcat	0.300	0.009	0.311
siamcat.to.lefse	0.026	0.003	0.029
siamcat.to.maaslin	0.027	0.003	0.030
summarize.features	1.856	0.200	2.070
train.model	39.211	0.663	40.122
validate.data	0.024	0.002	0.027
volcano.plot	0.014	0.004	0.018
weight_matrix-methods	0.007	0.002	0.012