Package: CEMiTool

Version: 1.4.2

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_1.4.2.tar.gz

StartedAt: 2018-10-16 20:20:46 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:25:52 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 305.9 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CEMiTool.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.2’
* 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  6.5Mb
  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
plot_interaction: no visible binding for global variable ‘cem’
filter_expr,CEMiTool: 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’
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 cem data dev.off dist
  hclust head tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "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 or elapsed time > 5s
                    user system elapsed
plot_ora          11.685  0.169  12.212
mod_ora           10.641  0.334  10.414
plot_interactions 10.726  0.176  11.090
ora_data          10.669  0.127  10.797
plot_gsea          6.764  0.192   4.077
gsea_data          5.041  0.470   3.757
mod_gsea           4.917  0.536   3.849
* 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-3.7-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/3.5/Resources/library’
* installing *source* package ‘CEMiTool’ ...
** 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
* DONE (CEMiTool)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 86 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 45.697   2.511  42.972 

name	user	system	elapsed
CEMiTool-class	0.022	0.007	0.033
adj_data	0.253	0.014	0.269
cem	0.027	0.006	0.032
cem_overlap	0.002	0.001	0.002
cemitool	0.003	0.000	0.003
expr0	0.002	0.001	0.004
expr_data	0.046	0.004	0.051
filter_expr	0.882	0.018	0.904
find_modules	3.940	0.030	4.008
fit_data	3.865	0.026	3.931
generate_report	0.001	0.001	0.001
geom_qq	0.002	0.000	0.002
get_adj	0.226	0.011	0.245
get_beta_data	1.942	0.040	2.005
get_cemitool_r2_beta	3.949	0.034	4.026
get_connectivity	3.912	0.030	3.975
get_hubs	0.025	0.005	0.029
get_merged_mods	2.225	0.019	2.271
get_mods	0.604	0.012	0.619
get_phi	3.675	0.020	3.719
gsea_data	5.041	0.470	3.757
interactions_data	0.909	0.231	0.469
mod_colors	0.024	0.005	0.029
mod_gsea	4.917	0.536	3.849
mod_names	0.095	0.026	0.024
mod_ora	10.641	0.334	10.414
mod_summary	0.108	0.014	0.079
module_genes	0.130	0.021	0.041
new_cem	0.088	0.007	0.024
nmodules	0.171	0.012	0.047
ora_data	10.669	0.127	10.797
plot_beta_r2	0.302	0.007	0.312
plot_gsea	6.764	0.192	4.077
plot_hist	0.681	0.035	0.729
plot_interactions	10.726	0.176	11.090
plot_mean_k	0.285	0.005	0.292
plot_mean_var	0.756	0.014	0.784
plot_ora	11.685	0.169	12.212
plot_profile	2.615	0.014	2.665
plot_qq	2.416	0.242	2.690
plot_sample_tree	0.873	0.028	0.917
read_gmt	1.561	0.028	1.616
sample_annot	0.003	0.001	0.004
sample_annotation	0.022	0.002	0.024
save_plots	0.067	0.005	0.072
show_plot	0.251	0.006	0.260
write_files	0.001	0.000	0.001