Package: CEMiTool

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.11.1.tar.gz

StartedAt: 2020-01-16 02:39:11 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:46:29 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 438.2 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.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:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.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 ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.11.1’
* package encoding: UTF-8
* 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 ‘CEMiTool’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata   2.8Mb
* 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 ... NOTE
flip_vector: no visible global function definition for ‘setNames’
select_genes: no visible global function definition for ‘var’
get_hubs,CEMiTool : <anonymous>: no visible global function definition
  for ‘head’
get_merged_mods,CEMiTool: no visible global function definition for
  ‘hclust’
get_merged_mods,CEMiTool: no visible global function definition for
  ‘as.dist’
get_mods,CEMiTool: no visible global function definition for ‘hclust’
get_mods,CEMiTool: no visible global function definition for ‘as.dist’
get_phi,CEMiTool: no visible global function definition for ‘tail’
get_phi,CEMiTool: no visible global function definition for ‘head’
mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’
mod_gene_num,CEMiTool: no visible binding for global variable
  ‘num_genes’
mod_summary,CEMiTool: no visible global function definition for ‘:=’
plot_gsea,CEMiTool: no visible global function definition for ‘hclust’
plot_gsea,CEMiTool: no visible global function definition for ‘dist’
plot_mean_var,CEMiTool: no visible binding for global variable ‘var’
plot_mean_var,CEMiTool: no visible binding for global variable ‘Mean’
plot_mean_var,CEMiTool: no visible binding for global variable
  ‘Variance’
plot_mean_var,CEMiTool: no visible binding for global variable
  ‘..eq.label..’
plot_mean_var,CEMiTool: no visible binding for global variable
  ‘..rr.label..’
plot_ora,CEMiTool : <anonymous>: no visible global function definition
  for ‘head’
plot_qq,CEMiTool: no visible binding for global variable ‘data’
plot_sample_tree,CEMiTool: no visible global function definition for
  ‘hclust’
plot_sample_tree,CEMiTool: no visible global function definition for
  ‘dist’
plot_sample_tree,CEMiTool: no visible global function definition for
  ‘dev.off’
save_plots,CEMiTool : <anonymous>: no visible global function
  definition for ‘dev.off’
save_plots,CEMiTool: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  ..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist
  hclust head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "setNames", "var")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
cemitool          16.818  0.705  17.900
plot_interactions 12.200  0.357  12.571
gsea_data          6.053  1.008   5.408
plot_ora           6.480  0.411   6.893
plot_gsea          5.153  0.993   4.490
mod_gsea           5.101  0.923   4.141
mod_ora            4.495  0.548   4.597
ora_data           4.666  0.349   4.851
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.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 CEMiTool
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CEMiTool’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** exec
** 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 (CEMiTool)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CEMiTool)

> test_check('CEMiTool')
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 105 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 55.857   6.830  52.047 

name	user	system	elapsed
CEMiTool-class	0.024	0.008	0.034
adj_data	1.219	0.041	1.260
cem	0.031	0.012	0.042
cemitool	16.818	0.705	17.900
expr0	0.001	0.002	0.003
expr_data	0.238	0.010	0.248
filter_expr	0.893	0.042	0.934
find_modules	2.611	0.083	2.693
fit_data	2.559	0.095	2.653
generate_report	0.000	0.000	0.001
get_adj	0.324	0.023	0.346
get_beta_data	1.068	0.025	1.092
get_cemitool_r2_beta	2.755	0.102	2.856
get_connectivity	2.733	0.083	2.816
get_hubs	0.026	0.010	0.035
get_merged_mods	1.582	0.043	1.626
get_mods	1.043	0.033	1.076
get_phi	2.715	0.084	2.800
gsea_data	6.053	1.008	5.408
interactions_data	1.916	0.131	0.704
mod_colors	0.018	0.007	0.025
mod_gene_num	0.188	0.013	0.200
mod_gsea	5.101	0.923	4.141
mod_names	0.061	0.039	0.025
mod_ora	4.495	0.548	4.597
mod_summary	0.466	0.164	0.354
module_genes	0.168	0.129	0.068
new_cem	0.086	0.070	0.036
nmodules	0.101	0.074	0.038
ora_data	4.666	0.349	4.851
plot_beta_r2	0.286	0.009	0.295
plot_gsea	5.153	0.993	4.490
plot_hist	0.772	0.040	0.812
plot_interactions	12.200	0.357	12.571
plot_mean_k	0.393	0.017	0.494
plot_mean_var	0.589	0.019	0.612
plot_ora	6.480	0.411	6.893
plot_profile	3.470	0.093	3.567
plot_qq	0.710	0.046	0.776
plot_sample_tree	1.118	0.051	1.183
read_gmt	1.397	0.049	1.481
sample_annot	0.005	0.004	0.010
sample_annotation	0.024	0.008	0.038
save_plots	0.049	0.016	0.074
select_genes	0.453	0.044	0.527
show_plot	0.322	0.018	0.403
write_files	2.300	1.048	1.402