Package: SIAMCAT

Version: 1.7.0

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_1.7.0.tar.gz

StartedAt: 2020-01-16 08:53:23 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:58:39 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 316.3 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.7.0’
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
train.model          33.711  0.253  34.428
evaluate.predictions 14.061  0.275  14.336
* 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-3.11-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/4.0/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	0.052	0.015	0.067
add.meta.pred	0.132	0.010	0.143
assign-associations	0.052	0.007	0.059
assign-data_split	0.025	0.003	0.029
assign-eval_data	0.028	0.007	0.035
assign-filt_feat	0.048	0.009	0.056
assign-label	0.026	0.003	0.029
assign-meta	0.053	0.003	0.057
assign-model_list	0.614	0.006	0.621
assign-norm_feat	0.024	0.001	0.025
assign-orig_feat	0.033	0.003	0.036
assign-physeq	0.027	0.004	0.031
assign-pred_matrix	0.028	0.008	0.035
assoc_param-methods	0.025	0.009	0.033
associations-methods	0.044	0.011	0.055
check.associations	0.374	0.019	0.435
check.confounders	0.835	0.062	0.904
create.data.split	0.098	0.023	0.122
create.label	0.009	0.003	0.012
data_split-methods	0.016	0.004	0.020
eval_data-methods	0.023	0.002	0.025
evaluate.predictions	14.061	0.275	14.336
feature_type-methods	0.021	0.003	0.025
feature_weights-methods	0.102	0.018	0.121
filt_feat-methods	0.023	0.003	0.027
filt_params-methods	0.023	0.006	0.030
filter.features	0.031	0.005	0.037
filter.label	0.028	0.008	0.036
get.filt_feat.matrix	0.025	0.008	0.034
get.norm_feat.matrix	0.041	0.006	0.046
get.orig_feat.matrix	0.023	0.002	0.025
label-methods	0.016	0.002	0.019
make.predictions	0.316	0.006	0.322
meta-methods	0.081	0.010	0.092
model.evaluation.plot	0.059	0.012	0.074
model.interpretation.plot	0.114	0.006	0.122
model_list-methods	0.022	0.002	0.024
model_type-methods	0.053	0.003	0.056
models-methods	0.026	0.002	0.028
norm_feat-methods	0.023	0.003	0.026
norm_params-methods	0.022	0.003	0.026
normalize.features	0.035	0.004	0.038
orig_feat-methods	0.043	0.004	0.047
physeq-methods	0.020	0.001	0.022
pred_matrix-methods	0.022	0.002	0.025
read.label	0.018	0.001	0.020
read.lefse	1.398	0.092	1.491
select.samples	0.191	0.004	0.194
siamcat	0.523	0.018	0.542
siamcat.to.lefse	0.593	0.025	0.639
siamcat.to.maaslin	0.035	0.005	0.040
summarize.features	0.640	0.029	0.671
train.model	33.711	0.253	34.428
validate.data	0.048	0.003	0.051
weight_matrix-methods	0.031	0.005	0.035