Package: CEMiTool

Version: 1.0.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_1.0.3.tar.gz

StartedAt: 2018-04-11 22:05:28 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:09:37 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 249.1 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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  8.8Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       2.4Mb
    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
plot_interactions 8.648  0.048   8.701
generate_report   7.672  0.844  11.674
* 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
  ‘/home/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-pc-linux-gnu (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 
 29.356   0.696  30.122 

name	user	system	elapsed
CEMiTool-class	0.028	0.004	0.032
adj_data	0.172	0.000	0.174
cem	0.028	0.000	0.027
cem_overlap	0.000	0.000	0.001
cemitool	0.000	0.000	0.001
expr	0.000	0.000	0.001
expr_data	0.284	0.004	0.289
filter_expr	0.596	0.000	0.596
find_modules	3.408	0.004	3.435
fit_data	3.696	0.012	3.708
generate_report	7.672	0.844	11.674
geom_qq	0.004	0.000	0.001
get_adj	0.208	0.016	0.226
get_beta_data	1.952	0.036	1.992
get_cemitool_r2_beta	2.984	0.004	2.987
get_connectivity	3.032	0.000	3.035
get_hubs	0.024	0.000	0.021
get_merged_mods	1.664	0.000	1.665
get_mods	0.460	0.004	0.464
get_phi	2.968	0.000	2.969
gsea_data	2.660	0.064	2.744
interactions_data	0.612	0.008	0.622
mod_colors	0.340	0.032	0.369
mod_gsea	2.672	0.004	2.677
mod_names	0.02	0.00	0.02
mod_ora	3.352	0.000	3.371
mod_summary	0.044	0.000	0.044
module_genes	0.024	0.000	0.025
new_cem	0.032	0.000	0.032
nmodules	0.02	0.00	0.02
ora_data	2.916	0.004	2.920
plot_beta_r2	1.184	0.000	1.188
plot_gsea	3.364	0.000	3.368
plot_hist	0.836	0.008	0.845
plot_interactions	8.648	0.048	8.701
plot_mean_k	0.220	0.000	0.221
plot_mean_var	0.552	0.016	0.625
plot_ora	3.768	0.004	3.778
plot_profile	1.7	0.0	1.7
plot_qq	2.156	0.020	2.178
plot_sample_tree	0.532	0.008	0.540
read_gmt	0.528	0.000	0.526
sample_annot	0.000	0.000	0.002
sample_annotation	0.044	0.004	0.048
save_plots	0.056	0.000	0.056
show_plot	0.156	0.000	0.158
write_files	0.112	0.000	0.112