Multiple platform build/check report for BioC 3.12 - CHECK report for SIAMCAT on merida1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIAMCAT_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘1.10.0’
* 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  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    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 ... NOTE
  Note: found 10 marked UTF-8 strings
* 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 25.571  0.157  25.777
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

Installation output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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	0.050	0.007	0.057
add.meta.pred	0.098	0.004	0.102
assign-associations	0.023	0.003	0.026
assign-data_split	0.040	0.004	0.043
assign-eval_data	0.027	0.003	0.031
assign-filt_feat	0.032	0.004	0.037
assign-label	0.033	0.003	0.037
assign-meta	0.061	0.003	0.065
assign-model_list	0.092	0.004	0.096
assign-norm_feat	0.029	0.002	0.030
assign-orig_feat	0.034	0.004	0.037
assign-physeq	0.027	0.002	0.030
assign-pred_matrix	0.037	0.003	0.039
assoc_param-methods	0.020	0.001	0.020
associations-methods	0.029	0.001	0.031
check.associations	0.711	0.017	0.731
check.confounders	0.618	0.035	0.658
create.data.split	0.065	0.004	0.069
create.label	0.005	0.002	0.008
data_split-methods	0.025	0.002	0.028
eval_data-methods	0.026	0.003	0.030
evaluate.predictions	3.127	0.083	3.222
feature_type-methods	0.022	0.002	0.024
feature_weights-methods	0.040	0.002	0.042
filt_feat-methods	0.042	0.005	0.048
filt_params-methods	0.023	0.001	0.025
filter.features	0.033	0.001	0.035
filter.label	0.027	0.003	0.030
get.filt_feat.matrix	0.023	0.002	0.025
get.norm_feat.matrix	0.030	0.002	0.033
get.orig_feat.matrix	0.021	0.002	0.023
label-methods	0.025	0.002	0.026
make.predictions	0.189	0.003	0.192
meta-methods	0.052	0.002	0.054
model.evaluation.plot	0.037	0.006	0.042
model.interpretation.plot	0.080	0.004	0.084
model_list-methods	0.031	0.002	0.034
model_type-methods	0.021	0.002	0.024
models-methods	0.025	0.002	0.027
norm_feat-methods	0.023	0.003	0.026
norm_params-methods	0.033	0.003	0.035
normalize.features	0.041	0.002	0.043
orig_feat-methods	0.023	0.002	0.024
physeq-methods	0.050	0.005	0.055
pred_matrix-methods	0.027	0.001	0.029
read.label	0.012	0.001	0.013
read.lefse	1.358	0.027	1.388
select.samples	0.086	0.004	0.089
siamcat	0.278	0.012	0.289
siamcat.to.lefse	0.064	0.007	0.071
siamcat.to.maaslin	0.041	0.004	0.045
summarize.features	1.960	0.154	2.118
train.model	25.571	0.157	25.777
validate.data	0.038	0.003	0.040
weight_matrix-methods	0.027	0.003	0.029

CHECK report for SIAMCAT on merida1

Summary

Command output

Installation output

Tests output

Example timings