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CHECK report for CEMiTool on tokay1

This page was generated on 2018-04-12 13:30:15 -0400 (Thu, 12 Apr 2018).

Package 199/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.0.3
Helder Nakaya
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_6
Last Commit: 366ec54
Last Changed Date: 2018-03-23 12:16:20 -0400 (Fri, 23 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

CEMiTool.Rcheck/00install.out


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

Tests output

CEMiTool.Rcheck/tests_i386/testthat.Rout


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 

CEMiTool.Rcheck/tests_x64/testthat.Rout


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 

Example timings

CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.070.000.07
adj_data0.370.020.53
cem0.260.000.26
cem_overlap000
cemitool000
expr0.000.010.02
expr_data0.020.020.03
filter_expr0.610.010.63
find_modules3.340.033.54
fit_data3.030.053.08
generate_report 4.88 0.5227.42
geom_qq000
get_adj0.200.030.24
get_beta_data1.700.011.72
get_cemitool_r2_beta2.750.052.79
get_connectivity3.040.003.03
get_hubs0.000.030.03
get_merged_mods1.480.031.52
get_mods0.420.000.42
get_phi2.560.002.56
gsea_data2.990.002.99
interactions_data0.970.001.01
mod_colors0.000.020.02
mod_gsea3.530.033.56
mod_names0.050.000.05
mod_ora3.960.064.03
mod_summary0.050.000.33
module_genes0.020.020.03
new_cem0.040.000.05
nmodules0.020.000.01
ora_data2.780.032.82
plot_beta_r20.950.010.96
plot_gsea3.340.003.34
plot_hist1.110.051.16
plot_interactions9.770.199.95
plot_mean_k0.200.010.22
plot_mean_var0.360.083.06
plot_ora3.330.003.58
plot_profile1.850.001.84
plot_qq2.650.222.88
plot_sample_tree0.640.030.76
read_gmt0.800.020.81
sample_annot000
sample_annotation0.020.010.04
save_plots0.040.000.04
show_plot0.180.000.17
write_files0.070.030.11

CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.020.030.05
adj_data0.810.020.82
cem0.050.000.05
cem_overlap000
cemitool000
expr000
expr_data0.030.000.03
filter_expr1.200.051.25
find_modules5.170.055.22
fit_data5.060.005.06
generate_report 5.94 0.3615.11
geom_qq000
get_adj0.810.000.82
get_beta_data2.300.002.29
get_cemitool_r2_beta4.810.004.82
get_connectivity4.360.004.36
get_hubs0.020.000.01
get_merged_mods2.160.002.15
get_mods0.610.000.61
get_phi4.070.004.08
gsea_data3.800.003.79
interactions_data1.170.011.19
mod_colors0.030.020.05
mod_gsea2.530.012.54
mod_names0.020.000.02
mod_ora4.200.024.22
mod_summary0.030.000.03
module_genes0.030.000.03
new_cem0.020.000.01
nmodules0.030.010.05
ora_data3.200.133.33
plot_beta_r20.850.000.84
plot_gsea3.320.003.33
plot_hist1.020.051.06
plot_interactions9.720.179.89
plot_mean_k0.230.010.25
plot_mean_var0.470.000.47
plot_ora3.670.023.69
plot_profile2.230.032.27
plot_qq3.270.223.48
plot_sample_tree0.870.000.88
read_gmt0.660.010.67
sample_annot0.000.020.02
sample_annotation0.020.000.01
save_plots0.070.000.08
show_plot0.250.000.25
write_files0.110.020.13