Package: CEMiTool

Version: 1.10.2

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CEMiTool_1.10.2.tar.gz

StartedAt: 2020-04-15 05:00:36 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:05:33 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 296.4 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CEMiTool_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CEMiTool.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.2’
* 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
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 or elapsed time > 5s
                    user system elapsed
cemitool          13.844  0.092  14.007
plot_interactions 10.220  0.088  10.403
gsea_data          7.720  0.276   5.388
plot_gsea          7.808  0.016   5.378
mod_gsea           6.408  0.016   4.047
write_files        5.156  0.012   2.369
plot_ora           4.968  0.008   5.018
* 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-3.10-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CEMiTool
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 105 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 56.248   0.716  44.412 

name	user	system	elapsed
CEMiTool-class	0.012	0.008	0.021
adj_data	0.308	0.000	0.309
cem	0.024	0.000	0.023
cemitool	13.844	0.092	14.007
expr0	0.000	0.000	0.001
expr_data	0.240	0.000	0.238
filter_expr	0.296	0.000	0.297
find_modules	2.152	0.004	2.160
fit_data	1.868	0.000	1.872
generate_report	0.000	0.000	0.001
get_adj	0.164	0.000	0.164
get_beta_data	0.840	0.000	0.858
get_cemitool_r2_beta	2.112	0.004	2.120
get_connectivity	1.696	0.000	1.697
get_hubs	0.02	0.00	0.02
get_merged_mods	1.180	0.004	1.199
get_mods	0.904	0.004	0.909
get_phi	1.808	0.000	1.807
gsea_data	7.720	0.276	5.388
interactions_data	0.444	0.016	0.474
mod_colors	0.028	0.000	0.028
mod_gene_num	0.084	0.004	0.090
mod_gsea	6.408	0.016	4.047
mod_names	0.048	0.000	0.050
mod_ora	3.512	0.008	3.527
mod_summary	2.244	0.008	0.780
module_genes	0.032	0.004	0.034
new_cem	0.020	0.000	0.023
nmodules	0.020	0.004	0.027
ora_data	3.504	0.000	3.523
plot_beta_r2	0.192	0.000	0.189
plot_gsea	7.808	0.016	5.378
plot_hist	0.580	0.004	0.584
plot_interactions	10.220	0.088	10.403
plot_mean_k	0.280	0.000	0.364
plot_mean_var	0.564	0.028	0.594
plot_ora	4.968	0.008	5.018
plot_profile	2.940	0.004	2.958
plot_qq	0.632	0.004	0.655
plot_sample_tree	0.828	0.008	0.851
read_gmt	0.988	0.000	0.995
sample_annot	0.004	0.000	0.003
sample_annotation	0.020	0.004	0.023
save_plots	0.056	0.000	0.056
select_genes	0.308	0.004	0.317
show_plot	0.240	0.004	0.249
write_files	5.156	0.012	2.369