Package: SIAMCAT

Version: 1.2.1

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_1.2.1.tar.gz

StartedAt: 2019-04-16 02:46:59 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:50:53 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 234.0 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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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          27.195  0.098  27.840
evaluate.predictions 16.425  0.070  16.948
* 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-3.8-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/3.5/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)

name	user	system	elapsed
accessSlot	0.044	0.010	0.055
add.meta.pred	0.287	0.016	0.317
assign-associations	0.054	0.003	0.058
assign-data_split	0.049	0.004	0.053
assign-eval_data	0.064	0.004	0.068
assign-filt_feat	0.052	0.002	0.053
assign-label	0.050	0.002	0.051
assign-meta	0.068	0.004	0.073
assign-model_list	0.049	0.002	0.051
assign-norm_feat	0.049	0.003	0.057
assign-orig_feat	0.052	0.002	0.054
assign-physeq	0.060	0.002	0.063
assign-pred_matrix	0.051	0.003	0.054
assoc_param-methods	0.015	0.001	0.016
associations-methods	0.036	0.004	0.041
check.associations	0.636	0.022	0.669
check.confounders	1.041	0.036	1.091
create.data.split	0.082	0.004	0.088
create.label	0.010	0.002	0.012
data_split-methods	0.057	0.011	0.068
eval_data-methods	0.040	0.016	0.057
evaluate.predictions	16.425	0.070	16.948
feature_type-methods	0.030	0.002	0.033
feature_weights-methods	0.042	0.004	0.049
filt_feat-methods	0.189	0.044	0.233
filt_params-methods	0.033	0.003	0.036
filter.features	0.057	0.001	0.059
filter.label	0.042	0.002	0.043
get.filt_feat.matrix	0.046	0.008	0.054
get.norm_feat.matrix	0.020	0.001	0.022
get.orig_feat.matrix	0.020	0.001	0.022
label-methods	0.033	0.004	0.036
make.predictions	0.264	0.003	0.267
meta-methods	0.045	0.005	0.050
model.evaluation.plot	0.030	0.003	0.033
model.interpretation.plot	0.114	0.004	0.119
model_list-methods	0.036	0.001	0.037
model_type-methods	0.020	0.001	0.022
models-methods	0.044	0.003	0.046
norm_feat-methods	0.158	0.035	0.192
norm_params-methods	0.019	0.002	0.022
normalize.features	0.130	0.002	0.148
orig_feat-methods	0.457	0.099	0.586
physeq-methods	0.433	0.004	0.439
pred_matrix-methods	0.020	0.002	0.022
read.label	0.009	0.000	0.010
read.lefse	1.639	0.064	1.748
select.samples	0.145	0.005	0.150
siamcat	0.474	0.017	0.493
siamcat.to.lefse	0.047	0.002	0.049
siamcat.to.maaslin	0.041	0.003	0.043
summarize.features	0.782	0.025	0.837
train.model	27.195	0.098	27.840
validate.data	0.075	0.002	0.087
weight_matrix-methods	0.038	0.004	0.041