Package: SIAMCAT

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 05:00:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:04:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 196.7 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_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SIAMCAT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 or elapsed time > 5s
                       user system elapsed
train.model          24.889  0.012  25.104
evaluate.predictions  7.739  0.004   7.759
* 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
** 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	0.037	0.004	0.051
add.meta.pred	0.115	0.004	0.121
assign-associations	0.025	0.000	0.026
assign-data_split	0.022	0.003	0.025
assign-eval_data	0.022	0.004	0.026
assign-filt_feat	0.026	0.000	0.026
assign-label	0.031	0.004	0.036
assign-meta	0.047	0.007	0.054
assign-model_list	0.028	0.000	0.028
assign-norm_feat	0.028	0.000	0.028
assign-orig_feat	0.045	0.000	0.045
assign-physeq	0.022	0.004	0.026
assign-pred_matrix	0.027	0.000	0.026
assoc_param-methods	0.023	0.000	0.024
associations-methods	0.040	0.000	0.039
check.associations	0.365	0.008	0.374
check.confounders	1.012	0.000	1.015
create.data.split	0.046	0.001	0.046
create.label	0.003	0.002	0.006
data_split-methods	0.039	0.000	0.039
eval_data-methods	0.025	0.000	0.025
evaluate.predictions	7.739	0.004	7.759
feature_type-methods	0.034	0.000	0.034
feature_weights-methods	0.032	0.000	0.032
filt_feat-methods	0.019	0.004	0.024
filt_params-methods	0.032	0.000	0.033
filter.features	0.027	0.000	0.027
filter.label	0.022	0.000	0.022
get.filt_feat.matrix	0.039	0.000	0.038
get.norm_feat.matrix	0.015	0.000	0.015
get.orig_feat.matrix	0.014	0.000	0.014
label-methods	0.023	0.000	0.023
make.predictions	0.149	0.000	0.150
meta-methods	0.039	0.000	0.039
model.evaluation.plot	0.031	0.000	0.032
model.interpretation.plot	0.087	0.000	0.087
model_list-methods	0.015	0.000	0.014
model_type-methods	0.010	0.004	0.014
models-methods	0.024	0.000	0.024
norm_feat-methods	0.015	0.000	0.014
norm_params-methods	0.014	0.000	0.014
normalize.features	0.031	0.003	0.034
orig_feat-methods	0.011	0.004	0.015
physeq-methods	0.017	0.000	0.018
pred_matrix-methods	0.023	0.000	0.023
read.label	0.008	0.000	0.017
read.lefse	1.221	0.012	1.256
select.samples	0.061	0.000	0.062
siamcat	0.321	0.004	0.325
siamcat.to.lefse	0.042	0.000	0.042
siamcat.to.maaslin	0.106	0.000	0.106
summarize.features	0.433	0.000	0.463
train.model	24.889	0.012	25.104
validate.data	0.040	0.003	0.044
weight_matrix-methods	0.027	0.000	0.027