Package: SIAMCAT

Version: 1.3.1

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_1.3.1.tar.gz

StartedAt: 2019-04-09 03:44:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:48:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 242.2 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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.1’
* 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          29.741  0.141  30.018
evaluate.predictions 16.716  0.054  17.000
* 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’ ...
** 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)

name	user	system	elapsed
accessSlot	0.042	0.007	0.059
add.meta.pred	0.174	0.005	0.183
assign-associations	0.035	0.003	0.039
assign-data_split	0.041	0.003	0.045
assign-eval_data	0.031	0.001	0.032
assign-filt_feat	0.032	0.002	0.033
assign-label	0.031	0.002	0.033
assign-meta	0.049	0.003	0.054
assign-model_list	0.042	0.002	0.044
assign-norm_feat	0.047	0.003	0.051
assign-orig_feat	0.052	0.001	0.057
assign-physeq	0.047	0.001	0.049
assign-pred_matrix	0.040	0.001	0.043
assoc_param-methods	0.021	0.002	0.022
associations-methods	0.043	0.003	0.047
check.associations	0.670	0.028	0.712
check.confounders	1.164	0.039	1.236
create.data.split	0.067	0.001	0.070
create.label	0.009	0.002	0.011
data_split-methods	0.043	0.009	0.052
eval_data-methods	0.037	0.017	0.058
evaluate.predictions	16.716	0.054	17.000
feature_type-methods	0.021	0.002	0.023
feature_weights-methods	0.061	0.005	0.066
filt_feat-methods	0.182	0.040	0.226
filt_params-methods	0.020	0.002	0.023
filter.features	0.066	0.003	0.069
filter.label	0.049	0.001	0.051
get.filt_feat.matrix	0.022	0.001	0.023
get.norm_feat.matrix	0.034	0.002	0.036
get.orig_feat.matrix	0.022	0.003	0.024
label-methods	0.047	0.008	0.055
make.predictions	0.268	0.002	0.275
meta-methods	0.040	0.005	0.049
model.evaluation.plot	0.045	0.002	0.048
model.interpretation.plot	0.113	0.003	0.119
model_list-methods	0.045	0.002	0.047
model_type-methods	0.021	0.001	0.022
models-methods	0.030	0.001	0.032
norm_feat-methods	0.182	0.036	0.220
norm_params-methods	0.022	0.002	0.024
normalize.features	0.117	0.002	0.119
orig_feat-methods	0.438	0.096	0.543
physeq-methods	0.026	0.001	0.027
pred_matrix-methods	0.026	0.003	0.029
read.label	0.031	0.000	0.032
read.lefse	1.579	0.024	1.613
select.samples	0.116	0.002	0.119
siamcat	0.409	0.013	0.427
siamcat.to.lefse	0.092	0.003	0.096
siamcat.to.maaslin	0.048	0.002	0.050
summarize.features	0.723	0.020	0.746
train.model	29.741	0.141	30.018
validate.data	0.073	0.002	0.075
weight_matrix-methods	0.032	0.004	0.037