Multiple platform build/check report for BioC 3.11 - CHECK report for CEMiTool on tokay2

Package: CEMiTool

Version: 1.12.2

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CEMiTool_1.12.2.tar.gz

StartedAt: 2020-10-17 02:27:07 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:34:52 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 465.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: CEMiTool.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CEMiTool_1.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.12.2'
* 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 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 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CEMiTool.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.7Mb
  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 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          9.45   0.17    9.78
plot_interactions 7.08   0.06    7.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
cemitool          11.45   0.25   11.70
plot_interactions  6.43   0.15    6.58
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-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/3.11/bioc/src/contrib/CEMiTool_1.12.2.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.12.2.zip && rm CEMiTool_1.12.2.tar.gz CEMiTool_1.12.2.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 4047k  100 4047k    0     0  39.6M      0 --:--:-- --:--:-- --:--:-- 41.6M

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
Warning: replacing previous import 'ggplot2::annotate' by 'ggpmisc::annotate' when loading 'CEMiTool'
** 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
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

install for x64

* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::annotate' by 'ggpmisc::annotate' when loading 'CEMiTool'
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.12.2.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)

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 
  37.87    1.07   39.17


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)

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 
  38.90    0.82   39.73

name	user	system	elapsed
CEMiTool-class	0.02	0.00	0.01
adj_data	0.67	0.00	0.67
cem	0.02	0.01	0.03
cemitool	9.45	0.17	9.78
expr0	0	0	0
expr_data	0.14	0.00	0.14
filter_expr	0.17	0.02	0.19
find_modules	1.45	0.01	1.47
fit_data	1.49	0.00	1.48
generate_report	0	0	0
get_adj	0.5	0.0	0.5
get_beta_data	0.61	0.00	0.61
get_cemitool_r2_beta	1.54	0.02	1.56
get_connectivity	1.80	0.00	3.05
get_hubs	0.03	0.00	0.03
get_merged_mods	0.89	0.00	1.21
get_mods	0.91	0.00	0.94
get_phi	1.70	0.03	1.94
gsea_data	3.95	0.00	3.95
interactions_data	0.42	0.00	1.87
mod_colors	0.05	0.00	0.05
mod_gene_num	0.19	0.02	0.47
mod_gsea	3.73	0.03	3.97
mod_names	0.02	0.01	0.03
mod_ora	2.53	0.07	3.33
mod_summary	0.16	0.00	0.16
module_genes	0.06	0.00	0.06
new_cem	0.05	0.01	0.07
nmodules	0.05	0.00	0.04
ora_data	2.78	0.00	2.78
plot_beta_r2	0.19	0.00	0.19
plot_gsea	3	0	3
plot_hist	0.34	0.02	0.36
plot_interactions	7.08	0.06	7.16
plot_mean_k	0.17	0.00	0.17
plot_mean_var	0.39	0.00	1.37
plot_ora	3.05	0.16	3.21
plot_profile	1.29	0.00	1.29
plot_qq	0.44	0.01	0.46
plot_sample_tree	0.80	0.06	0.86
read_gmt	0.75	0.00	0.75
sample_annot	0.00	0.02	0.01
sample_annotation	0.01	0.00	0.02
save_plots	0.05	0.00	0.04
select_genes	0.20	0.00	0.21
show_plot	0.14	0.00	0.14
write_files	0.83	0.00	0.83

name	user	system	elapsed
CEMiTool-class	0.06	0.00	0.07
adj_data	0.39	0.04	0.42
cem	0.02	0.00	0.19
cemitool	11.45	0.25	11.70
expr0	0.00	0.01	0.02
expr_data	0.14	0.00	0.14
filter_expr	0.3	0.0	0.3
find_modules	2.06	0.02	2.37
fit_data	2.40	0.01	2.61
generate_report	0	0	0
get_adj	0.18	0.00	0.17
get_beta_data	0.76	0.01	0.78
get_cemitool_r2_beta	2.48	0.00	3.04
get_connectivity	2.30	0.00	2.33
get_hubs	0.00	0.02	0.17
get_merged_mods	1.14	0.01	1.36
get_mods	0.97	0.00	0.97
get_phi	2.33	0.02	2.52
gsea_data	3.92	0.00	4.98
interactions_data	0.25	0.03	0.28
mod_colors	0.01	0.02	0.03
mod_gene_num	0.24	0.01	0.49
mod_gsea	3.08	0.02	3.09
mod_names	0.01	0.00	0.02
mod_ora	2.60	0.06	3.06
mod_summary	0.25	0.03	0.37
module_genes	0.01	0.02	0.04
new_cem	0.06	0.00	0.06
nmodules	0.04	0.00	0.03
ora_data	3.35	0.00	3.56
plot_beta_r2	0.15	0.00	0.14
plot_gsea	3.01	0.00	3.19
plot_hist	0.34	0.00	0.34
plot_interactions	6.43	0.15	6.58
plot_mean_k	0.28	0.00	0.28
plot_mean_var	0.45	0.00	0.45
plot_ora	3.08	0.05	3.13
plot_profile	1.45	0.01	1.47
plot_qq	0.49	0.00	0.48
plot_sample_tree	1.31	0.00	1.31
read_gmt	0.61	0.00	0.61
sample_annot	0.02	0.00	0.01
sample_annotation	0.02	0.00	0.02
save_plots	0.03	0.00	0.03
select_genes	0.17	0.00	0.17
show_plot	0.17	0.00	0.17
write_files	0.83	0.03	0.86

CHECK report for CEMiTool on tokay2

Summary

Command output

Installation output

Tests output

Example timings