Build/check report for BioC 3.17 - CHECK results for SIAMCAT on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4266
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-3.17-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SIAMCAT_2.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.3.0’
* 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         28.336  0.540  28.881
make.predictions          28.099  0.439  28.541
model.interpretation.plot 28.131  0.372  28.504
train.model               27.039  0.228  27.267
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SIAMCAT_confounder.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_holdout.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_meta.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_ml_pitfalls.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_read-in.Rmd’ using ‘ASCII’... OK
  ‘SIAMCAT_vignette.Rmd’ using ‘ASCII’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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	0.011	0.000	0.011
add.meta.pred	0.034	0.000	0.034
assign-associations	0.005	0.005	0.010
assign-data_split	0.005	0.004	0.009
assign-eval_data	0.009	0.000	0.009
assign-filt_feat	0.009	0.000	0.010
assign-label	0.005	0.004	0.009
assign-meta	0.036	0.000	0.036
assign-model_list	28.336	0.540	28.881
assign-norm_feat	0.009	0.000	0.009
assign-orig_feat	0.015	0.000	0.015
assign-physeq	0.010	0.000	0.009
assign-pred_matrix	0.005	0.003	0.009
assoc_param-methods	0.003	0.004	0.007
association.plot	0.301	0.032	0.334
associations-methods	0.012	0.000	0.012
check.associations	2.42	0.02	2.44
check.confounders	0.561	0.003	0.565
create.data.split	0.028	0.001	0.028
create.label	0.003	0.000	0.002
data_split-methods	0.007	0.000	0.007
eval_data-methods	0.007	0.000	0.008
evaluate.predictions	0.028	0.000	0.029
feature_type-methods	0.007	0.000	0.008
feature_weights-methods	0.007	0.000	0.007
filt_feat-methods	0.007	0.000	0.007
filt_params-methods	0.007	0.000	0.007
filter.features	0.04	0.00	0.04
filter.label	0.01	0.00	0.01
get.filt_feat.matrix	0.007	0.000	0.008
get.norm_feat.matrix	0.007	0.000	0.008
get.orig_feat.matrix	0.007	0.000	0.008
label-methods	0.007	0.000	0.008
make.predictions	28.099	0.439	28.541
meta-methods	0.024	0.000	0.024
model.evaluation.plot	0.03	0.00	0.03
model.interpretation.plot	28.131	0.372	28.504
model_list-methods	0.007	0.000	0.007
model_type-methods	0.007	0.000	0.007
models-methods	0.007	0.000	0.007
norm_feat-methods	0.007	0.000	0.007
norm_params-methods	0.007	0.001	0.007
normalize.features	0.015	0.003	0.017
orig_feat-methods	0.008	0.000	0.008
physeq-methods	0.012	0.000	0.012
pred_matrix-methods	0.003	0.004	0.007
read.label	0.006	0.004	0.011
read.lefse	0.918	0.012	0.932
select.samples	0.080	0.001	0.081
siamcat	0.322	0.010	0.332
siamcat.to.lefse	0.021	0.000	0.022
siamcat.to.maaslin	0.023	0.000	0.023
summarize.features	2.806	0.044	2.850
train.model	27.039	0.228	27.267
validate.data	0.024	0.000	0.024
volcano.plot	0.015	0.000	0.015
weight_matrix-methods	0.007	0.000	0.007

CHECK results for SIAMCAT on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings