Multiple platform build/check report for BioC 3.7 - CHECK report for SIAMCAT on merida2

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### Running command:
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###   /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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.0’
* 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 ... OK
* 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 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
train.model          19.501  0.173  19.767
evaluate.predictions 12.674  0.063  12.833
* 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: OK

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SIAMCAT’ ...
** 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
* DONE (SIAMCAT)

Tests output

Example timings

name	user	system	elapsed
accessSlot	0.062	0.013	0.077
add.meta.pred	0.214	0.012	0.226
assign-data_split	0.043	0.003	0.046
assign-eval_data	0.035	0.003	0.038
assign-features	0.062	0.004	0.066
assign-label	0.125	0.014	0.140
assign-meta	0.040	0.004	0.045
assign-model_list	0.046	0.004	0.050
assign-norm_param	0.034	0.002	0.037
assign-orig_feat	0.031	0.003	0.033
assign-physeq	0.033	0.001	0.035
assign-pred_matrix	0.030	0.003	0.033
check.associations	2.297	0.048	2.377
check.confounders	1.235	0.022	1.270
create.data.split	0.059	0.003	0.062
create.label.from.metadata	0.038	0.002	0.040
data_split-methods	0.071	0.013	0.085
eval_data-methods	0.072	0.011	0.084
evaluate.predictions	12.674	0.063	12.833
features-methods	0.447	0.106	0.558
filter.features	0.067	0.003	0.069
filter.label	0.034	0.002	0.035
get.features.matrix	0.027	0.005	0.032
get.orig_feat.matrix	0.038	0.004	0.042
label-methods	0.039	0.004	0.042
make.predictions	3.050	0.012	3.078
meta-methods	0.050	0.009	0.060
model.evaluation.plot	0.047	0.004	0.053
model.interpretation.plot	0.099	0.006	0.109
model_list-methods	0.038	0.004	0.041
model_type-methods	0.045	0.004	0.049
models-methods	0.036	0.002	0.040
norm_param-methods	0.031	0.003	0.034
normalize.features	0.144	0.004	0.155
orig_feat-methods	0.066	0.013	0.079
physeq-methods	0.038	0.003	0.041
pred_matrix-methods	0.041	0.005	0.045
read.features	0.247	0.007	0.260
read.labels	0.013	0.000	0.014
read.meta	0.004	0.000	0.004
reset.features	0.046	0.002	0.050
select.samples	0.048	0.001	0.049
siamcat	0.231	0.012	0.245
train.model	19.501	0.173	19.767
validate.data	0.086	0.003	0.088

CHECK report for SIAMCAT on merida2

Summary

Command output

Installation output

Tests output

Example timings