Package: CEMiTool

Version: 1.7.7

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CEMiTool_1.7.7.tar.gz

StartedAt: 2019-04-09 01:39:24 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:46:43 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 439.2 seconds

RetCode: 0

Status:  OK

CheckDir: CEMiTool.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CEMiTool_1.7.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CEMiTool.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.7.7'
* 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
cem_overlap : <anonymous>: no visible binding for global variable
  'splitBy'
cem_overlap: no visible binding for global variable 'object'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable 'gene'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable 'P.Value'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'median'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'sd'
flip_vector: no visible global function definition for 'setNames'
makeContMatrix: no visible global function definition for
  'model.matrix'
makeLimmaComp: no visible global function definition for 'setNames'
mod_activity : <anonymous>: no visible binding for global variable
  'modules'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'gene'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'comparison'
mod_activity : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'logFC'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'module'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'fc_median'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'parameter'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable 'value'
mod_activity : <anonymous>: no visible binding for global variable
  'new_col'
mod_activity : <anonymous>: no visible binding for global variable
  'comparison'
mod_activity : <anonymous>: no visible binding for global variable
  'parameter'
mod_activity : <anonymous>: no visible binding for global variable
  'value'
mod_compare : <anonymous>: no visible binding for global variable
  'modules'
mod_compare: no visible binding for global variable 'first_mod'
mod_compare: no visible binding for global variable 'second_mod'
mod_compare: no visible global function definition for 'p.adjust'
mod_compare: no visible binding for global variable 'Jaccard'
mod_compare: no visible binding for global variable 'Fisherp'
mod_compare: no visible binding for global variable 'fdr'
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable 'value'
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable 'pathway'
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable 'module'
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable 'metric'
mod_info : <anonymous>: no visible binding for global variable 'metric'
mod_info : <anonymous>: no visible binding for global variable
  'modules'
mod_info : <anonymous>: no visible binding for global variable 'module'
mod_info: no visible binding for global variable 'value'
mod_info: no visible binding for global variable 'module'
plot_comembership: no visible binding for global variable 'Var1'
plot_comembership: no visible binding for global variable 'Freq'
plot_consensus: no visible global function definition for 'sd'
plot_consensus: no visible binding for global variable 'X1'
plot_consensus: no visible binding for global variable 'Y1'
plot_consensus: no visible binding for global variable 'X2'
plot_consensus: no visible binding for global variable 'Y2'
plot_consensus: no visible binding for global variable 'Communities'
plot_similarity: no visible binding for global variable 'X1'
plot_similarity: no visible binding for global variable 'Y1'
plot_similarity: no visible binding for global variable 'X2'
plot_similarity: no visible binding for global variable 'Y2'
plot_similarity: no visible binding for global variable 'Weight'
plot_similarity: no visible binding for global variable 'Names'
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'
mod_summary,CEMiTool: no visible global function definition for ':='
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.. := Communities Fisherp Freq Jaccard Mean
  Names P.Value Var1 Variance Weight X1 X2 Y1 Y2 as.dist comparison
  data dev.off dist fc_median fdr first_mod gene hclust head logFC
  median metric model.matrix module modules new_col object p.adjust
  parameter pathway sd second_mod setNames splitBy tail value var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "median",
             "model.matrix", "p.adjust", "sd", "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 or elapsed time > 5s
                   user system elapsed
plot_interactions 12.25   0.16   12.41
cemitool           6.83   0.11    6.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_interactions 9.18   0.20    9.39
cemitool          9.03   0.10   10.24
plot_ora          5.92   0.11    6.03
* 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-3.9-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/3.9/bioc/src/contrib/CEMiTool_1.7.7.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.7.7.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.7.7.zip && rm CEMiTool_1.7.7.tar.gz CEMiTool_1.7.7.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100 4057k  100 4057k    0     0  41.0M      0 --:--:-- --:--:-- --:--:-- 44.0M

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  
    enrich_mods                             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  
    makeContMatrix                          html  
    makeLimmaComp                           html  
    mod_activity                            html  
    mod_colors                              html  
    mod_compare                             html  
    mod_gsea                                html  
    mod_info                                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  
    outer_join_merge                        html  
    overlap_community                       html  
    plot_beta_r2                            html  
    plot_comembership                       html  
    plot_consensus                          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  
    plot_similarity                         html  
    read_gmt                                html  
    sample_annot                            html  
    sample_annotation                       html  
    save_plots                              html  
    show-CEMiTool-method                    html  
    show_plot                               html  
    stat_overlap_mods                       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_1.7.7.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 94 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  35.75    2.67   38.32 

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 94 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  35.10    1.07   36.15