Package: CEMiTool

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CEMiTool_1.0.3.tar.gz

StartedAt: 2018-04-12 01:25:15 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:29:51 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 276.2 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 --no-vignettes --timings CEMiTool_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.3’
* 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  8.9Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       2.6Mb
    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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
generate_report   10.235  1.452  16.416
plot_interactions 10.514  0.175  10.910
* 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-3.6-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.

* installing *source* package ‘CEMiTool’ ...
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CEMiTool)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
 31.591   1.600  32.761 

name	user	system	elapsed
CEMiTool-class	0.028	0.006	0.038
adj_data	0.460	0.013	0.487
cem	0.024	0.005	0.029
cem_overlap	0.001	0.000	0.001
cemitool	0.001	0.001	0.001
expr	0.001	0.001	0.002
expr_data	0.028	0.004	0.032
filter_expr	0.531	0.022	0.559
find_modules	3.484	0.033	3.573
fit_data	4.050	0.039	4.155
generate_report	10.235	1.452	16.416
geom_qq	0.001	0.000	0.001
get_adj	0.423	0.005	0.434
get_beta_data	1.352	0.013	1.389
get_cemitool_r2_beta	2.787	0.020	2.851
get_connectivity	2.897	0.024	2.945
get_hubs	0.019	0.003	0.022
get_merged_mods	1.684	0.013	1.716
get_mods	0.540	0.012	0.571
get_phi	2.933	0.017	3.037
gsea_data	3.766	0.271	3.336
interactions_data	1.200	0.129	0.990
mod_colors	0.026	0.003	0.030
mod_gsea	3.845	0.270	3.402
mod_names	0.048	0.011	0.032
mod_ora	4.190	0.130	4.249
mod_summary	0.054	0.007	0.051
module_genes	0.068	0.013	0.042
new_cem	0.030	0.006	0.018
nmodules	0.399	0.034	0.325
ora_data	3.800	0.058	3.967
plot_beta_r2	1.031	0.017	1.074
plot_gsea	4.450	0.176	4.117
plot_hist	1.011	0.048	1.089
plot_interactions	10.514	0.175	10.910
plot_mean_k	0.283	0.005	0.292
plot_mean_var	0.539	0.018	0.572
plot_ora	4.500	0.194	4.775
plot_profile	2.310	0.013	2.373
plot_qq	2.329	0.199	2.572
plot_sample_tree	0.723	0.020	0.757
read_gmt	0.801	0.011	0.843
sample_annot	0.003	0.002	0.005
sample_annotation	0.025	0.007	0.032
save_plots	0.071	0.004	0.074
show_plot	0.210	0.004	0.219
write_files	0.143	0.008	0.150