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 05:29:16 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:34:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 304.7 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) (2019-03-18 r76245)
* 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          30.168  0.167  31.352
evaluate.predictions 20.514  0.160  21.194
* 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
*** 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)

name	user	system	elapsed
accessSlot	0.054	0.019	0.073
add.meta.pred	0.316	0.010	0.327
assign-associations	0.061	0.009	0.070
assign-data_split	0.069	0.011	0.080
assign-eval_data	0.036	0.003	0.039
assign-filt_feat	0.056	0.004	0.073
assign-label	0.052	0.003	0.087
assign-meta	0.097	0.005	0.116
assign-model_list	0.055	0.002	0.057
assign-norm_feat	0.052	0.005	0.057
assign-orig_feat	0.053	0.006	0.058
assign-physeq	0.064	0.002	0.066
assign-pred_matrix	0.052	0.003	0.055
assoc_param-methods	0.022	0.004	0.026
associations-methods	0.050	0.007	0.057
check.associations	0.754	0.067	0.823
check.confounders	1.478	0.079	1.562
create.data.split	0.103	0.007	0.110
create.label	0.011	0.002	0.013
data_split-methods	0.059	0.025	0.082
eval_data-methods	0.056	0.040	0.096
evaluate.predictions	20.514	0.160	21.194
feature_type-methods	0.022	0.002	0.024
feature_weights-methods	0.072	0.007	0.080
filt_feat-methods	0.201	0.081	0.283
filt_params-methods	0.022	0.003	0.026
filter.features	0.090	0.005	0.098
filter.label	0.055	0.002	0.058
get.filt_feat.matrix	0.020	0.001	0.023
get.norm_feat.matrix	0.043	0.002	0.045
get.orig_feat.matrix	0.019	0.003	0.021
label-methods	0.064	0.019	0.087
make.predictions	0.323	0.007	0.340
meta-methods	0.046	0.012	0.058
model.evaluation.plot	0.064	0.004	0.071
model.interpretation.plot	0.126	0.007	0.136
model_list-methods	0.063	0.004	0.068
model_type-methods	0.020	0.001	0.022
models-methods	0.031	0.003	0.034
norm_feat-methods	0.222	0.075	0.308
norm_params-methods	0.021	0.002	0.023
normalize.features	0.130	0.003	0.193
orig_feat-methods	0.592	0.237	0.838
physeq-methods	0.020	0.002	0.022
pred_matrix-methods	0.019	0.005	0.023
read.label	0.037	0.001	0.038
read.lefse	2.005	0.055	2.067
select.samples	0.172	0.003	0.174
siamcat	1.004	0.035	1.040
siamcat.to.lefse	0.049	0.003	0.062
siamcat.to.maaslin	0.051	0.003	0.088
summarize.features	0.861	0.036	0.899
train.model	30.168	0.167	31.352
validate.data	0.082	0.002	0.090
weight_matrix-methods	0.033	0.007	0.041