Multiple platform build/check report for BioC 3.19 - CHECK results for SIAMCAT on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SIAMCAT_2.7.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.7.2’
* 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 ... OK
* 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 loading without being on the library search path ... 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         20.310  0.920  21.230
train.model               19.596  0.256  19.852
model.interpretation.plot 19.355  0.320  19.675
make.predictions          19.365  0.244  19.610
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SIAMCAT
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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	0.534	0.020	0.554
add.meta.pred	0.029	0.000	0.029
assign-associations	0.006	0.000	0.006
assign-data_split	0.007	0.000	0.007
assign-eval_data	0.003	0.004	0.007
assign-filt_feat	0.003	0.004	0.007
assign-label	0.006	0.000	0.006
assign-meta	0.023	0.004	0.027
assign-model_list	20.31	0.92	21.23
assign-norm_feat	0.007	0.000	0.006
assign-orig_feat	0.011	0.000	0.011
assign-physeq	0.002	0.003	0.007
assign-pred_matrix	0.006	0.000	0.006
assoc_param-methods	0.015	0.000	0.014
association.plot	0.214	0.004	0.217
associations-methods	0.009	0.000	0.008
check.associations	0.01	0.00	0.01
check.confounders	0.405	0.020	0.426
create.data.split	0.016	0.004	0.020
create.label	0.002	0.000	0.003
data_split-methods	0.001	0.003	0.006
eval_data-methods	0.017	0.009	0.026
evaluate.predictions	1.418	0.003	1.422
feature_type-methods	0.005	0.000	0.006
feature_weights-methods	0.005	0.000	0.006
filt_feat-methods	0.005	0.000	0.005
filt_params-methods	0.005	0.000	0.005
filter.features	0.013	0.000	0.013
filter.label	0.007	0.000	0.007
get.filt_feat.matrix	0.054	0.007	0.061
get.norm_feat.matrix	0.006	0.001	0.006
get.orig_feat.matrix	0.005	0.000	0.006
label-methods	0.006	0.000	0.006
make.predictions	19.365	0.244	19.610
meta-methods	0.016	0.003	0.021
model.evaluation.plot	0.022	0.005	0.025
model.interpretation.plot	19.355	0.320	19.675
model_list-methods	0.006	0.000	0.005
model_type-methods	0.006	0.000	0.005
models-methods	0.001	0.004	0.005
norm_feat-methods	0.002	0.003	0.005
norm_params-methods	0.004	0.000	0.005
normalize.features	0.009	0.003	0.013
orig_feat-methods	0.006	0.001	0.006
physeq-methods	0.009	0.000	0.009
pred_matrix-methods	0.002	0.004	0.006
read.label	0.004	0.004	0.007
read.lefse	0.619	0.007	0.627
select.samples	0.055	0.000	0.055
siamcat	0.268	0.004	0.271
siamcat.to.lefse	0.018	0.003	0.022
siamcat.to.maaslin	0.024	0.000	0.024
summarize.features	1.384	0.020	1.403
train.model	19.596	0.256	19.852
validate.data	0.015	0.003	0.018
volcano.plot	0.012	0.000	0.012
weight_matrix-methods	0.006	0.000	0.005

CHECK results for SIAMCAT on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings