Multiple platform build/check report for BioC 3.20 - CHECK results for SIAMCAT on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 kjohnson3

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: 2.10.0

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_2.10.0.tar.gz

StartedAt: 2024-11-09 13:21:05 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 13:26:18 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 312.1 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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
make.predictions          6.651  0.109   6.760
assign-model_list         6.526  0.120   6.649
train.model               6.461  0.138   6.601
model.interpretation.plot 6.353  0.139   6.492
* 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/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	0.002	0.001	0.005
add.meta.pred	0.171	0.001	0.172
assign-associations	0.002	0.001	0.002
assign-data_split	0.002	0.000	0.002
assign-eval_data	0.002	0.001	0.003
assign-filt_feat	0.002	0.000	0.003
assign-label	0.002	0.001	0.003
assign-meta	0.007	0.001	0.007
assign-model_list	6.526	0.120	6.649
assign-norm_feat	0.003	0.001	0.003
assign-orig_feat	0.003	0.001	0.005
assign-physeq	0.002	0.001	0.003
assign-pred_matrix	0.008	0.001	0.009
assoc_param-methods	0.003	0.000	0.003
association.plot	0.079	0.004	0.083
associations-methods	0.003	0.001	0.004
check.associations	0.004	0.000	0.004
check.confounders	0.136	0.008	0.144
create.data.split	0.017	0.002	0.019
create.label	0.001	0.000	0.001
data_split-methods	0.003	0.001	0.002
eval_data-methods	0.002	0.000	0.003
evaluate.predictions	0.512	0.039	0.552
feature_type-methods	0.003	0.000	0.003
feature_weights-methods	0.002	0.001	0.003
filt_feat-methods	0.002	0.001	0.003
filt_params-methods	0.002	0.000	0.003
filter.features	0.004	0.001	0.006
filter.label	0.002	0.001	0.003
get.filt_feat.matrix	0.003	0.001	0.003
get.norm_feat.matrix	0.002	0.001	0.003
get.orig_feat.matrix	0.002	0.001	0.003
label-methods	0.002	0.001	0.003
make.predictions	6.651	0.109	6.760
meta-methods	0.007	0.001	0.008
model.evaluation.plot	0.008	0.002	0.010
model.interpretation.plot	6.353	0.139	6.492
model_list-methods	0.007	0.001	0.007
model_type-methods	0.002	0.000	0.003
models-methods	0.003	0.000	0.003
norm_feat-methods	0.002	0.001	0.003
norm_params-methods	0.002	0.001	0.003
normalize.features	0.007	0.001	0.007
orig_feat-methods	0.002	0.000	0.003
physeq-methods	0.004	0.001	0.005
pred_matrix-methods	0.002	0.001	0.002
read.label	0.003	0.000	0.003
read.lefse	0.191	0.006	0.198
select.samples	0.014	0.001	0.015
siamcat	0.317	0.008	0.325
siamcat.to.lefse	0.007	0.000	0.008
siamcat.to.maaslin	0.007	0.000	0.008
summarize.features	0.591	0.049	0.640
train.model	6.461	0.138	6.601
validate.data	0.006	0.001	0.006
volcano.plot	0.004	0.001	0.005
weight_matrix-methods	0.002	0.001	0.003