Multiple platform build/check report for BioC 3.7 - CHECK report for CEMiTool on tokay2

Package: CEMiTool

Version: 1.4.2

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CEMiTool_1.4.2.tar.gz

StartedAt: 2018-10-17 00:59:29 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:08:05 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 516.6 seconds

RetCode: 0

Status: OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CEMiTool_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CEMiTool.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.4.2'
* 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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mod_ora              10.50   0.12   10.63
ora_data              9.72   0.06    9.78
plot_interactions     9.26   0.13    9.39
plot_ora              8.61   0.02    8.62
fit_data              5.27   0.02    5.28
get_cemitool_r2_beta  5.15   0.00    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ora_data          9.45   0.01    9.47
plot_ora          8.53   0.02    8.55
mod_ora           7.74   0.07    7.80
plot_interactions 7.66   0.13    7.78
find_modules      6.06   0.01    6.08
gsea_data         3.41   0.03   21.62
* 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-3.7-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CEMiTool_1.4.2.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.4.2.zip && rm CEMiTool_1.4.2.tar.gz CEMiTool_1.4.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4046k  100 4046k    0     0  33.1M      0 --:--:-- --:--:-- --:--:-- 34.9M

install for i386

* installing *source* package 'CEMiTool' ...
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare 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  
    expr0                                   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  
    module_to_gmt                           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_1.4.2.zip
* DONE (CEMiTool)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  35.53    1.71   37.20


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  46.62    1.53   48.14

name	user	system	elapsed
CEMiTool-class	0.06	0.03	0.09
adj_data	0.27	0.00	0.36
cem	0.03	0.02	0.05
cem_overlap	0	0	0
cemitool	0	0	0
expr0	0.00	0.01	0.02
expr_data	0.04	0.00	0.04
filter_expr	0.47	0.00	0.47
find_modules	4.55	0.08	4.67
fit_data	5.27	0.02	5.28
generate_report	0	0	0
geom_qq	0	0	0
get_adj	0.21	0.01	0.24
get_beta_data	1.93	0.00	1.92
get_cemitool_r2_beta	5.15	0.00	5.16
get_connectivity	4.36	0.02	4.37
get_hubs	0.03	0.00	0.03
get_merged_mods	2.50	0.03	2.53
get_mods	0.64	0.02	0.66
get_phi	4.30	0.01	4.31
gsea_data	3.69	0.24	4.02
interactions_data	0.50	0.06	0.56
mod_colors	0.03	0.00	0.03
mod_gsea	4.37	0.00	4.37
mod_names	0.03	0.00	0.03
mod_ora	10.50	0.12	10.63
mod_summary	0.10	0.00	0.09
module_genes	0.04	0.00	0.05
new_cem	0.02	0.02	0.03
nmodules	0.14	0.00	0.14
ora_data	9.72	0.06	9.78
plot_beta_r2	0.40	0.02	1.33
plot_gsea	4.33	0.01	4.34
plot_hist	0.60	0.03	0.63
plot_interactions	9.26	0.13	9.39
plot_mean_k	0.22	0.00	0.22
plot_mean_var	0.5	0.0	0.5
plot_ora	8.61	0.02	8.62
plot_profile	2.05	0.00	2.05
plot_qq	3.21	0.09	3.31
plot_sample_tree	0.75	0.08	0.97
read_gmt	1.04	0.00	1.03
sample_annot	0	0	0
sample_annotation	0.01	0.00	0.02
save_plots	0.05	0.00	0.05
show_plot	0.17	0.01	0.18
write_files	0	0	0

name	user	system	elapsed
CEMiTool-class	0.03	0.01	0.04
adj_data	0.31	0.03	0.35
cem	0.02	0.03	0.05
cem_overlap	0	0	0
cemitool	0.02	0.00	0.01
expr0	0	0	0
expr_data	0.03	0.03	0.07
filter_expr	0.64	0.05	0.68
find_modules	6.06	0.01	6.08
fit_data	4.23	0.00	4.24
generate_report	0	0	0
geom_qq	0	0	0
get_adj	0.14	0.00	0.14
get_beta_data	2.15	0.07	2.20
get_cemitool_r2_beta	4.31	0.00	4.31
get_connectivity	4.69	0.01	4.71
get_hubs	0.03	0.00	0.03
get_merged_mods	2.42	0.00	2.42
get_mods	0.67	0.00	0.67
get_phi	4.25	0.02	4.27
gsea_data	3.41	0.03	21.62
interactions_data	0.35	0.01	0.36
mod_colors	0.01	0.02	0.03
mod_gsea	2.81	0.01	2.83
mod_names	0.05	0.00	0.04
mod_ora	7.74	0.07	7.80
mod_summary	0.04	0.00	0.05
module_genes	0.05	0.01	0.06
new_cem	0.01	0.02	0.03
nmodules	0.07	0.00	0.06
ora_data	9.45	0.01	9.47
plot_beta_r2	0.22	0.02	0.24
plot_gsea	3.12	0.00	3.12
plot_hist	0.66	0.06	0.72
plot_interactions	7.66	0.13	7.78
plot_mean_k	0.20	0.01	0.22
plot_mean_var	0.53	0.00	0.53
plot_ora	8.53	0.02	8.55
plot_profile	2.58	0.01	2.59
plot_qq	3.78	0.24	4.02
plot_sample_tree	0.67	0.03	0.70
read_gmt	0.47	0.02	0.48
sample_annot	0	0	0
sample_annotation	0.01	0.00	0.02
save_plots	0.07	0.00	0.06
show_plot	0.25	0.00	0.25
write_files	0	0	0

CHECK report for CEMiTool on tokay2

Summary

Command output

Installation output

Tests output

Example timings