Package: SIAMCAT

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 06:51:28 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:56:25 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 297.0 seconds

RetCode: 0

Status:  OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

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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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 ... 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 or elapsed time > 5s
                       user system elapsed
train.model          33.965  0.188  35.572
evaluate.predictions 12.476  0.174  13.153
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

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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/3.6/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
** 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)

name	user	system	elapsed
accessSlot	0.044	0.014	0.059
add.meta.pred	0.133	0.008	0.142
assign-associations	0.024	0.002	0.025
assign-data_split	0.025	0.004	0.028
assign-eval_data	0.024	0.007	0.031
assign-filt_feat	0.023	0.006	0.029
assign-label	0.029	0.002	0.031
assign-meta	0.051	0.002	0.054
assign-model_list	0.026	0.003	0.029
assign-norm_feat	0.025	0.003	0.028
assign-orig_feat	0.055	0.005	0.059
assign-physeq	0.025	0.004	0.029
assign-pred_matrix	0.025	0.005	0.030
assoc_param-methods	0.021	0.002	0.024
associations-methods	0.047	0.004	0.050
check.associations	0.429	0.025	0.461
check.confounders	1.334	0.092	1.437
create.data.split	0.059	0.014	0.074
create.label	0.009	0.004	0.014
data_split-methods	0.032	0.002	0.034
eval_data-methods	0.024	0.003	0.028
evaluate.predictions	12.476	0.174	13.153
feature_type-methods	0.051	0.011	0.064
feature_weights-methods	0.043	0.004	0.046
filt_feat-methods	0.023	0.004	0.030
filt_params-methods	0.046	0.007	0.056
filter.features	0.034	0.007	0.040
filter.label	0.024	0.002	0.030
get.filt_feat.matrix	0.046	0.003	0.050
get.norm_feat.matrix	0.020	0.004	0.024
get.orig_feat.matrix	0.058	0.013	0.073
label-methods	0.024	0.003	0.026
make.predictions	0.329	0.007	0.401
meta-methods	0.049	0.003	0.054
model.evaluation.plot	0.049	0.007	0.056
model.interpretation.plot	0.150	0.009	0.168
model_list-methods	0.023	0.002	0.025
model_type-methods	0.023	0.002	0.024
models-methods	0.053	0.003	0.056
norm_feat-methods	0.024	0.003	0.026
norm_params-methods	0.025	0.005	0.029
normalize.features	0.064	0.004	0.068
orig_feat-methods	0.023	0.002	0.024
physeq-methods	0.031	0.004	0.034
pred_matrix-methods	0.049	0.004	0.052
read.label	0.019	0.001	0.022
read.lefse	1.618	0.071	1.719
select.samples	0.094	0.005	0.099
siamcat	0.459	0.034	0.493
siamcat.to.lefse	0.031	0.002	0.032
siamcat.to.maaslin	0.090	0.014	0.105
summarize.features	0.671	0.028	0.698
train.model	33.965	0.188	35.572
validate.data	0.038	0.003	0.040
weight_matrix-methods	0.025	0.003	0.027