Package: CEMiTool

Version: 1.7.7

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_1.7.7.tar.gz

StartedAt: 2019-04-09 00:30:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:37:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 402.4 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_1.7.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CEMiTool.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.7’
* 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  6.6Mb
  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
cem_overlap : <anonymous>: no visible binding for global variable
  ‘splitBy’
cem_overlap: no visible binding for global variable ‘object’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘gene’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘P.Value’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘median’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘sd’
flip_vector: no visible global function definition for ‘setNames’
makeContMatrix: no visible global function definition for
  ‘model.matrix’
makeLimmaComp: no visible global function definition for ‘setNames’
mod_activity : <anonymous>: no visible binding for global variable
  ‘modules’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘gene’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘comparison’
mod_activity : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘logFC’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘module’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘fc_median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘parameter’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘value’
mod_activity : <anonymous>: no visible binding for global variable
  ‘new_col’
mod_activity : <anonymous>: no visible binding for global variable
  ‘comparison’
mod_activity : <anonymous>: no visible binding for global variable
  ‘parameter’
mod_activity : <anonymous>: no visible binding for global variable
  ‘value’
mod_compare : <anonymous>: no visible binding for global variable
  ‘modules’
mod_compare: no visible binding for global variable ‘first_mod’
mod_compare: no visible binding for global variable ‘second_mod’
mod_compare: no visible global function definition for ‘p.adjust’
mod_compare: no visible binding for global variable ‘Jaccard’
mod_compare: no visible binding for global variable ‘Fisherp’
mod_compare: no visible binding for global variable ‘fdr’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘value’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘pathway’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘module’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable
  ‘modules’
mod_info : <anonymous>: no visible binding for global variable ‘module’
mod_info: no visible binding for global variable ‘value’
mod_info: no visible binding for global variable ‘module’
plot_comembership: no visible binding for global variable ‘Var1’
plot_comembership: no visible binding for global variable ‘Freq’
plot_consensus: no visible global function definition for ‘sd’
plot_consensus: no visible binding for global variable ‘X1’
plot_consensus: no visible binding for global variable ‘Y1’
plot_consensus: no visible binding for global variable ‘X2’
plot_consensus: no visible binding for global variable ‘Y2’
plot_consensus: no visible binding for global variable ‘Communities’
plot_similarity: no visible binding for global variable ‘X1’
plot_similarity: no visible binding for global variable ‘Y1’
plot_similarity: no visible binding for global variable ‘X2’
plot_similarity: no visible binding for global variable ‘Y2’
plot_similarity: no visible binding for global variable ‘Weight’
plot_similarity: no visible binding for global variable ‘Names’
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’
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.. := Communities Fisherp Freq Jaccard Mean
  Names P.Value Var1 Variance Weight X1 X2 Y1 Y2 as.dist comparison
  data dev.off dist fc_median fdr first_mod gene hclust head logFC
  median metric model.matrix module modules new_col object p.adjust
  parameter pathway sd second_mod setNames splitBy tail value var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "median",
             "model.matrix", "p.adjust", "sd", "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 or elapsed time > 5s
                    user system elapsed
plot_interactions 11.974  0.401  12.852
cemitool          10.065  0.585  10.661
plot_gsea          6.410  1.262   4.057
gsea_data          5.727  0.863   4.132
mod_gsea           5.274  0.811   3.507
plot_ora           5.516  0.413   6.134
* 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-3.9-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/3.6/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) (2019-03-18 r76245) -- "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: 94 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 51.812  10.696  45.966 

name	user	system	elapsed
CEMiTool-class	0.024	0.009	0.033
adj_data	0.845	0.035	0.882
cem	0.025	0.009	0.034
cem_overlap	0.001	0.000	0.001
cemitool	10.065	0.585	10.661
enrich_mods	0.000	0.000	0.001
expr0	0.002	0.002	0.004
expr_data	0.045	0.016	0.059
filter_expr	0.406	0.041	0.447
find_modules	1.585	0.038	1.624
fit_data	1.454	0.036	1.490
generate_report	0	0	0
get_adj	0.269	0.016	0.285
get_beta_data	1.052	0.057	1.110
get_cemitool_r2_beta	1.549	0.045	1.595
get_connectivity	1.543	0.042	1.584
get_hubs	0.025	0.009	0.034
get_merged_mods	0.954	0.041	0.996
get_mods	0.800	0.015	0.815
get_phi	1.594	0.040	1.634
gsea_data	5.727	0.863	4.132
interactions_data	0.816	0.426	0.593
makeContMatrix	0.000	0.000	0.001
makeLimmaComp	0.001	0.001	0.002
mod_colors	0.037	0.016	0.053
mod_gsea	5.274	0.811	3.507
mod_names	0.062	0.055	0.027
mod_ora	4.213	0.540	4.385
mod_summary	0.207	0.102	0.138
module_genes	0.209	0.210	0.062
new_cem	0.111	0.111	0.032
nmodules	0.109	0.111	0.032
ora_data	3.646	0.451	3.737
overlap_community	0.000	0.000	0.001
plot_beta_r2	0.221	0.008	0.229
plot_comembership	0.000	0.001	0.001
plot_consensus	0	0	0
plot_gsea	6.410	1.262	4.057
plot_hist	0.652	0.076	0.728
plot_interactions	11.974	0.401	12.852
plot_mean_k	0.353	0.011	0.365
plot_mean_var	0.449	0.024	0.474
plot_ora	5.516	0.413	6.134
plot_profile	3.219	0.093	3.529
plot_qq	3.046	0.473	3.537
plot_sample_tree	0.912	0.105	1.072
plot_similarity	0.001	0.001	0.001
read_gmt	1.336	0.047	1.428
sample_annot	0.005	0.004	0.009
sample_annotation	0.021	0.004	0.025
save_plots	0.042	0.008	0.049
show_plot	0.327	0.023	0.350
stat_overlap_mods	0.000	0.001	0.001
write_files	0.411	0.263	0.213