Multiple platform build/check report for BioC 3.13 - CHECK results for CEMiTool on tokay2

Package: CEMiTool

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CEMiTool_1.16.0.tar.gz

StartedAt: 2021-10-14 20:52:07 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:58:53 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 406.1 seconds

RetCode: 0

Status: OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CEMiTool_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CEMiTool.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.16.0'
* 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  6.9Mb
  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
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 LazyData ... 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 (user + system) or elapsed time > 5s
                  user system elapsed
cemitool          7.69   0.30     8.0
plot_interactions 6.82   0.25     7.1
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
cemitool          9.47   0.08    9.55
plot_interactions 5.72   0.16    5.87
* 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-3.13-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CEMiTool_1.16.0.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.16.0.zip && rm CEMiTool_1.16.0.tar.gz CEMiTool_1.16.0.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
 43 4048k   43 1749k    0     0  2240k      0  0:00:01 --:--:--  0:00:01 2240k
100 4048k  100 4048k    0     0  2826k      0  0:00:01  0:00:01 --:--:-- 2827k

install for i386

* 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
  converting help for package 'CEMiTool'
    finding HTML links ... done
    CEMiTool-class                          html  
    adj_data                                html  
    cem                                     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  
    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  
    gsea_data                               html  
    interactions_data                       html  
    mod_colors                              html  
    mod_gene_num                            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  
    select_genes                            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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.16.0.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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')
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 105 ]
> 
> proc.time()
   user  system elapsed 
  25.89    1.14   27.00


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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')
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 105 ]
> 
> proc.time()
   user  system elapsed 
  26.32    0.96   27.28

name	user	system	elapsed
CEMiTool-class	0.02	0.00	0.01
adj_data	0.72	0.01	0.74
cem	0.03	0.00	0.03
cemitool	7.69	0.30	8.00
expr0	0	0	0
expr_data	0.09	0.00	0.10
filter_expr	0.11	0.01	0.12
find_modules	1.38	0.00	1.38
fit_data	1.37	0.00	1.37
generate_report	0	0	0
get_adj	0.07	0.02	0.08
get_beta_data	0.60	0.01	0.62
get_cemitool_r2_beta	1.46	0.00	1.46
get_connectivity	1.44	0.00	1.43
get_hubs	0.01	0.00	0.02
get_merged_mods	0.78	0.02	0.80
get_mods	0.66	0.00	0.65
get_phi	1.37	0.00	1.38
gsea_data	1.86	0.02	1.87
interactions_data	0.21	0.00	0.35
mod_colors	0.01	0.00	0.01
mod_gene_num	0.10	0.03	0.13
mod_gsea	1.60	0.00	1.61
mod_names	0.02	0.00	0.01
mod_ora	2.36	0.14	2.52
mod_summary	0.12	0.00	0.12
module_genes	0.05	0.01	0.07
new_cem	0.05	0.00	0.04
nmodules	0.05	0.02	0.07
ora_data	2.32	0.00	2.32
plot_beta_r2	0.12	0.00	0.12
plot_gsea	1.75	0.00	1.75
plot_hist	0.32	0.01	0.33
plot_interactions	6.82	0.25	7.10
plot_mean_k	0.16	0.00	0.15
plot_mean_var	0.31	0.04	0.46
plot_ora	3.07	0.16	3.22
plot_profile	1.32	0.01	1.34
plot_qq	0.46	0.00	0.46
plot_sample_tree	0.64	0.03	0.67
read_gmt	0.54	0.00	0.55
sample_annot	0	0	0
sample_annotation	0.04	0.00	0.03
save_plots	0.03	0.00	0.03
select_genes	0.14	0.00	0.14
show_plot	0.14	0.00	0.14
write_files	0.34	0.04	0.37

name	user	system	elapsed
CEMiTool-class	0.02	0.00	0.01
adj_data	0.22	0.03	0.25
cem	0.06	0.02	0.08
cemitool	9.47	0.08	9.55
expr0	0	0	0
expr_data	0.09	0.01	0.11
filter_expr	0.13	0.02	0.14
find_modules	1.65	0.00	1.65
fit_data	1.6	0.0	1.6
generate_report	0	0	0
get_adj	0.11	0.00	0.11
get_beta_data	0.68	0.01	0.70
get_cemitool_r2_beta	1.60	0.02	1.61
get_connectivity	1.61	0.00	1.61
get_hubs	0.03	0.00	0.03
get_merged_mods	0.83	0.02	0.84
get_mods	0.75	0.00	0.75
get_phi	1.62	0.00	1.63
gsea_data	1.95	0.01	1.97
interactions_data	0.22	0.00	0.22
mod_colors	0.02	0.00	0.01
mod_gene_num	0.09	0.02	0.11
mod_gsea	1.47	0.01	1.49
mod_names	0.02	0.02	0.03
mod_ora	2.04	0.01	2.06
mod_summary	0.13	0.00	0.13
module_genes	0.03	0.00	0.03
new_cem	0.02	0.00	0.01
nmodules	0.01	0.00	0.02
ora_data	2.50	0.02	2.51
plot_beta_r2	0.11	0.00	0.11
plot_gsea	1.56	0.01	1.58
plot_hist	0.27	0.00	0.27
plot_interactions	5.72	0.16	5.87
plot_mean_k	0.17	0.00	0.17
plot_mean_var	0.28	0.00	0.29
plot_ora	2.95	0.19	3.14
plot_profile	1.47	0.00	1.47
plot_qq	0.46	0.00	0.45
plot_sample_tree	0.75	0.00	0.75
read_gmt	0.64	0.01	0.65
sample_annot	0.00	0.02	0.02
sample_annotation	0.01	0.00	0.02
save_plots	0.03	0.00	0.03
select_genes	0.27	0.00	0.26
show_plot	0.17	0.03	0.21
write_files	0.5	0.0	0.5

CHECK results for CEMiTool on tokay2

Summary

Command output

Installation output

Tests output

Example timings