Multiple platform build/check report for BioC 3.11 - CHECK report for CEMiTool on machv2

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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_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.12.2’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::annotate’ by ‘ggpmisc::annotate’ when loading ‘CEMiTool’
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.Rcheck/00install.out’ for details.
* 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
  ‘as.dist’
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 ‘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
  ‘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
  head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "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 (user + system) or elapsed time > 5s
                    user system elapsed
gsea_data         15.787  0.046  15.846
plot_gsea         15.166  0.025  15.204
mod_gsea          14.950  0.030  14.998
cemitool          14.642  0.293  14.948
plot_interactions  9.535  0.183   9.778
plot_ora           5.527  0.148   5.721
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.

Installation output

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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/4.0/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
Warning: replacing previous import ‘ggplot2::annotate’ by ‘ggpmisc::annotate’ when loading ‘CEMiTool’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ggplot2::annotate’ by ‘ggpmisc::annotate’ when loading ‘CEMiTool’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ggplot2::annotate’ by ‘ggpmisc::annotate’ when loading ‘CEMiTool’
** testing if installed package keeps a record of temporary installation path
* DONE (CEMiTool)

Tests output


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)

Warning message:
replacing previous import 'ggplot2::annotate' by 'ggpmisc::annotate' when loading 'CEMiTool' 
> test_check('CEMiTool')
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 105 | SKIPPED: 0 | WARNINGS: 14 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 42.925   1.111  44.053

Example timings

name	user	system	elapsed
CEMiTool-class	0.053	0.002	0.057
adj_data	0.525	0.023	0.550
cem	0.459	0.011	0.472
cemitool	14.642	0.293	14.948
expr0	0.001	0.002	0.003
expr_data	0.256	0.005	0.261
filter_expr	0.358	0.010	0.370
find_modules	2.399	0.022	2.426
fit_data	2.369	0.028	2.398
generate_report	0	0	0
get_adj	0.656	0.008	0.665
get_beta_data	0.790	0.010	0.801
get_cemitool_r2_beta	2.264	0.015	2.281
get_connectivity	2.229	0.023	2.257
get_hubs	0.031	0.005	0.035
get_merged_mods	1.331	0.017	1.350
get_mods	1.003	0.010	1.014
get_phi	2.462	0.017	2.480
gsea_data	15.787	0.046	15.846
interactions_data	0.351	0.020	0.371
mod_colors	0.028	0.002	0.030
mod_gene_num	0.202	0.011	0.213
mod_gsea	14.950	0.030	14.998
mod_names	0.029	0.002	0.031
mod_ora	4.072	0.134	4.208
mod_summary	0.658	0.009	0.666
module_genes	0.034	0.008	0.042
new_cem	0.025	0.003	0.028
nmodules	0.022	0.002	0.025
ora_data	3.624	0.083	3.709
plot_beta_r2	0.697	0.011	0.708
plot_gsea	15.166	0.025	15.204
plot_hist	0.664	0.007	0.702
plot_interactions	9.535	0.183	9.778
plot_mean_k	0.253	0.005	0.257
plot_mean_var	0.534	0.016	0.550
plot_ora	5.527	0.148	5.721
plot_profile	2.500	0.018	2.522
plot_qq	0.645	0.026	0.673
plot_sample_tree	1.155	0.012	1.169
read_gmt	1.147	0.010	1.158
sample_annot	0.002	0.002	0.005
sample_annotation	0.027	0.005	0.031
save_plots	0.066	0.004	0.070
select_genes	0.346	0.006	0.352
show_plot	0.207	0.008	0.215
write_files	1.253	0.039	1.292

CHECK report for CEMiTool on machv2

Summary

Command output

Installation output

Tests output

Example timings