Package: SIAMCAT

Version: 1.0.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SIAMCAT_1.0.0.tar.gz

StartedAt: 2018-10-16 03:45:04 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:47:31 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 147.2 seconds

RetCode: 0

Status:  OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SIAMCAT_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 ... OK
* 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          13.932  0.020  13.981
evaluate.predictions  7.888  0.004   7.896
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	0.040	0.004	0.045
add.meta.pred	0.164	0.008	0.172
assign-data_split	0.040	0.000	0.039
assign-eval_data	0.028	0.000	0.029
assign-features	0.048	0.000	0.048
assign-label	0.112	0.000	0.112
assign-meta	0.044	0.000	0.041
assign-model_list	0.032	0.000	0.035
assign-norm_param	0.036	0.000	0.036
assign-orig_feat	0.028	0.000	0.027
assign-physeq	0.028	0.008	0.035
assign-pred_matrix	0.028	0.000	0.028
check.associations	1.580	0.004	1.583
check.confounders	0.804	0.004	0.809
create.data.split	0.048	0.000	0.051
create.label.from.metadata	0.040	0.000	0.041
data_split-methods	0.056	0.004	0.061
eval_data-methods	0.400	0.000	0.401
evaluate.predictions	7.888	0.004	7.896
features-methods	0.176	0.028	0.205
filter.features	0.040	0.008	0.046
filter.label	0.024	0.008	0.031
get.features.matrix	0.032	0.000	0.030
get.orig_feat.matrix	0.036	0.000	0.035
label-methods	0.028	0.004	0.031
make.predictions	2.072	0.004	2.079
meta-methods	0.032	0.004	0.037
model.evaluation.plot	0.032	0.004	0.035
model.interpretation.plot	0.076	0.004	0.079
model_list-methods	0.032	0.000	0.033
model_type-methods	0.044	0.000	0.041
models-methods	0.032	0.004	0.034
norm_param-methods	0.028	0.000	0.028
normalize.features	0.140	0.000	0.156
orig_feat-methods	0.064	0.004	0.068
physeq-methods	0.040	0.000	0.041
pred_matrix-methods	0.028	0.004	0.031
read.features	0.120	0.004	0.134
read.labels	0.008	0.000	0.015
read.meta	0.004	0.000	0.008
reset.features	0.044	0.000	0.041
select.samples	0.044	0.000	0.045
siamcat	0.136	0.008	0.141
train.model	13.932	0.020	13.981
validate.data	0.064	0.000	0.064