Multiple platform build/check report for BioC 3.6 - CHECK report for CEMiTool on tokay1

Package: CEMiTool

Version: 1.0.3

Command: rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_1.0.3.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_1.0.3.tar.gz

StartedAt: 2018-04-11 22:47:29 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:56:01 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 511.7 seconds

RetCode: 0

Status: OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_1.0.3.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       1.1Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_interactions 9.77   0.19    9.95
generate_report   4.88   0.52   27.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_interactions 9.72   0.17    9.89
generate_report   5.94   0.36   15.11
find_modules      5.17   0.05    5.22
fit_data          5.06   0.00    5.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'CEMiTool' ...
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CEMiTool'
    finding HTML links ... done
    CEMiTool-class                          html  
    adj_data                                html  
    cem                                     html  
    cem_overlap                             html  
    cemitool                                html  
    diagnostic_report                       html  
    expr                                    html  
    expr_data                               html  
    expr_pct_filter                         html  
    filter_expr                             html  
    find_modules                            html  
    fit_data                                html  
    generate_report                         html  
    geom_qq                                 html  
    get_adj                                 html  
    get_beta_data                           html  
    get_cemitool_r2_beta                    html  
    get_connectivity                        html  
    get_hubs                                html  
    get_merged_mods                         html  
    get_mods                                html  
    get_phi                                 html  
    ggplot2-ggproto                         html  
    gsea_data                               html  
    interactions_data                       html  
    mod_colors                              html  
    mod_gsea                                html  
    mod_names                               html  
    mod_ora                                 html  
    mod_summary                             html  
    module_genes                            html  
    new_cem                                 html  
    nmodules                                html  
    ora_data                                html  
    plot_beta_r2                            html  
    plot_gsea                               html  
    plot_hist                               html  
    plot_interactions                       html  
    plot_mean_k                             html  
    plot_mean_var                           html  
    plot_ora                                html  
    plot_ora_single                         html  
    plot_profile                            html  
    plot_qq                                 html  
    plot_sample_tree                        html  
    read_gmt                                html  
    sample_annot                            html  
    sample_annotation                       html  
    save_plots                              html  
    show-CEMiTool-method                    html  
    show_plot                               html  
    vst                                     html  
    write_files                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.0.3.zip
* DONE (CEMiTool)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  29.03    1.29   30.31


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  29.60    1.25   30.85

name	user	system	elapsed
CEMiTool-class	0.07	0.00	0.07
adj_data	0.37	0.02	0.53
cem	0.26	0.00	0.26
cem_overlap	0	0	0
cemitool	0	0	0
expr	0.00	0.01	0.02
expr_data	0.02	0.02	0.03
filter_expr	0.61	0.01	0.63
find_modules	3.34	0.03	3.54
fit_data	3.03	0.05	3.08
generate_report	4.88	0.52	27.42
geom_qq	0	0	0
get_adj	0.20	0.03	0.24
get_beta_data	1.70	0.01	1.72
get_cemitool_r2_beta	2.75	0.05	2.79
get_connectivity	3.04	0.00	3.03
get_hubs	0.00	0.03	0.03
get_merged_mods	1.48	0.03	1.52
get_mods	0.42	0.00	0.42
get_phi	2.56	0.00	2.56
gsea_data	2.99	0.00	2.99
interactions_data	0.97	0.00	1.01
mod_colors	0.00	0.02	0.02
mod_gsea	3.53	0.03	3.56
mod_names	0.05	0.00	0.05
mod_ora	3.96	0.06	4.03
mod_summary	0.05	0.00	0.33
module_genes	0.02	0.02	0.03
new_cem	0.04	0.00	0.05
nmodules	0.02	0.00	0.01
ora_data	2.78	0.03	2.82
plot_beta_r2	0.95	0.01	0.96
plot_gsea	3.34	0.00	3.34
plot_hist	1.11	0.05	1.16
plot_interactions	9.77	0.19	9.95
plot_mean_k	0.20	0.01	0.22
plot_mean_var	0.36	0.08	3.06
plot_ora	3.33	0.00	3.58
plot_profile	1.85	0.00	1.84
plot_qq	2.65	0.22	2.88
plot_sample_tree	0.64	0.03	0.76
read_gmt	0.80	0.02	0.81
sample_annot	0	0	0
sample_annotation	0.02	0.01	0.04
save_plots	0.04	0.00	0.04
show_plot	0.18	0.00	0.17
write_files	0.07	0.03	0.11

name	user	system	elapsed
CEMiTool-class	0.02	0.03	0.05
adj_data	0.81	0.02	0.82
cem	0.05	0.00	0.05
cem_overlap	0	0	0
cemitool	0	0	0
expr	0	0	0
expr_data	0.03	0.00	0.03
filter_expr	1.20	0.05	1.25
find_modules	5.17	0.05	5.22
fit_data	5.06	0.00	5.06
generate_report	5.94	0.36	15.11
geom_qq	0	0	0
get_adj	0.81	0.00	0.82
get_beta_data	2.30	0.00	2.29
get_cemitool_r2_beta	4.81	0.00	4.82
get_connectivity	4.36	0.00	4.36
get_hubs	0.02	0.00	0.01
get_merged_mods	2.16	0.00	2.15
get_mods	0.61	0.00	0.61
get_phi	4.07	0.00	4.08
gsea_data	3.80	0.00	3.79
interactions_data	1.17	0.01	1.19
mod_colors	0.03	0.02	0.05
mod_gsea	2.53	0.01	2.54
mod_names	0.02	0.00	0.02
mod_ora	4.20	0.02	4.22
mod_summary	0.03	0.00	0.03
module_genes	0.03	0.00	0.03
new_cem	0.02	0.00	0.01
nmodules	0.03	0.01	0.05
ora_data	3.20	0.13	3.33
plot_beta_r2	0.85	0.00	0.84
plot_gsea	3.32	0.00	3.33
plot_hist	1.02	0.05	1.06
plot_interactions	9.72	0.17	9.89
plot_mean_k	0.23	0.01	0.25
plot_mean_var	0.47	0.00	0.47
plot_ora	3.67	0.02	3.69
plot_profile	2.23	0.03	2.27
plot_qq	3.27	0.22	3.48
plot_sample_tree	0.87	0.00	0.88
read_gmt	0.66	0.01	0.67
sample_annot	0.00	0.02	0.02
sample_annotation	0.02	0.00	0.01
save_plots	0.07	0.00	0.08
show_plot	0.25	0.00	0.25
write_files	0.11	0.02	0.13

CHECK report for CEMiTool on tokay1

Summary

Command output

Installation output

Tests output

Example timings