Package: SIAMCAT

Version: 1.3.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIAMCAT_1.3.1.tar.gz

StartedAt: 2019-04-09 03:38:11 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:41:36 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 205.6 seconds

RetCode: 0

Status:  OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SIAMCAT_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.1’
* 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          22.281  0.028  22.416
evaluate.predictions 13.785  0.031  13.836
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SIAMCAT
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	0.046	0.000	0.052
add.meta.pred	0.248	0.004	0.252
assign-associations	0.574	0.000	0.575
assign-data_split	0.045	0.000	0.045
assign-eval_data	0.043	0.004	0.047
assign-filt_feat	0.036	0.012	0.047
assign-label	0.028	0.012	0.040
assign-meta	0.061	0.000	0.061
assign-model_list	0.038	0.000	0.038
assign-norm_feat	0.039	0.000	0.039
assign-orig_feat	0.041	0.000	0.041
assign-physeq	0.049	0.000	0.049
assign-pred_matrix	0.045	0.000	0.045
assoc_param-methods	0.021	0.000	0.022
associations-methods	0.031	0.000	0.031
check.associations	0.967	0.000	0.973
check.confounders	1.034	0.028	1.074
create.data.split	0.064	0.016	0.080
create.label	0.009	0.000	0.009
data_split-methods	0.038	0.004	0.045
eval_data-methods	0.030	0.008	0.038
evaluate.predictions	13.785	0.031	13.836
feature_type-methods	0.021	0.000	0.021
feature_weights-methods	0.029	0.004	0.034
filt_feat-methods	0.089	0.004	0.093
filt_params-methods	0.016	0.000	0.015
filter.features	0.044	0.000	0.044
filter.label	0.029	0.000	0.029
get.filt_feat.matrix	0.014	0.000	0.014
get.norm_feat.matrix	0.014	0.000	0.014
get.orig_feat.matrix	0.015	0.000	0.015
label-methods	0.02	0.00	0.02
make.predictions	0.254	0.004	0.257
meta-methods	0.030	0.004	0.034
model.evaluation.plot	0.033	0.000	0.034
model.interpretation.plot	0.106	0.000	0.105
model_list-methods	0.032	0.000	0.033
model_type-methods	0.022	0.000	0.022
models-methods	0.045	0.000	0.044
norm_feat-methods	0.090	0.016	0.107
norm_params-methods	0.023	0.000	0.022
normalize.features	0.087	0.004	0.091
orig_feat-methods	0.187	0.020	0.207
physeq-methods	0.017	0.000	0.016
pred_matrix-methods	0.023	0.004	0.026
read.label	0.010	0.000	0.015
read.lefse	0.824	0.012	0.849
select.samples	0.211	0.000	0.211
siamcat	0.48	0.00	0.48
siamcat.to.lefse	0.087	0.000	0.087
siamcat.to.maaslin	0.056	0.000	0.056
summarize.features	0.641	0.012	0.662
train.model	22.281	0.028	22.416
validate.data	0.075	0.000	0.092
weight_matrix-methods	0.033	0.000	0.033