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CHECK report for CEMiTool on tokay1

This page was generated on 2020-08-13 11:42:38 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CEMiTool PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 250/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.13.1
Helder Nakaya
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: master
Last Commit: 18c5654
Last Changed Date: 2020-07-02 12:14:01 -0400 (Thu, 02 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CEMiTool
Version: 1.13.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CEMiTool_1.13.1.tar.gz
StartedAt: 2020-08-13 04:22:43 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 04:30:00 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 436.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CEMiTool_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CEMiTool.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.13.1'
* 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  6.7Mb
  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          10.84   0.17   11.08
plot_interactions  7.53   0.16    7.69
plot_ora           4.86   0.11    5.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
cemitool          17.25   0.12   17.37
plot_interactions  8.34   0.19    8.53
plot_ora           5.24   0.14    5.37
* 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-3.12-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.



Installation output

CEMiTool.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CEMiTool_1.13.1.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.13.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.13.1.zip && rm CEMiTool_1.13.1.tar.gz CEMiTool_1.13.1.zip
###
##############################################################################
##############################################################################


  % 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  44.8M      0 --:--:-- --:--:-- --:--:-- 47.0M

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_1.13.1.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked

Tests output

CEMiTool.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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)

> test_check('CEMiTool')
== testthat results  ===========================================================
[ OK: 105 | SKIPPED: 0 | WARNINGS: 20 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  39.18    1.59   40.81 

CEMiTool.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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)

> test_check('CEMiTool')
== testthat results  ===========================================================
[ OK: 105 | SKIPPED: 0 | WARNINGS: 20 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  29.45    0.59   30.06 

Example timings

CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.010.020.04
adj_data0.670.000.67
cem0.040.000.03
cemitool10.84 0.1711.08
expr0000
expr_data0.250.010.30
filter_expr0.620.000.62
find_modules1.890.021.91
fit_data1.780.001.78
generate_report000
get_adj0.560.020.58
get_beta_data0.610.000.61
get_cemitool_r2_beta2.360.012.37
get_connectivity1.630.001.63
get_hubs0.030.000.03
get_merged_mods0.840.000.84
get_mods0.750.000.75
get_phi2.220.022.23
gsea_data4.090.014.11
interactions_data0.380.020.75
mod_colors0.030.000.03
mod_gene_num0.220.010.24
mod_gsea3.420.033.45
mod_names0.010.000.02
mod_ora3.30.13.4
mod_summary0.190.000.19
module_genes0.050.000.05
new_cem0.060.000.06
nmodules0.030.000.03
ora_data2.660.032.69
plot_beta_r20.160.000.15
plot_gsea2.900.002.91
plot_hist0.380.000.37
plot_interactions7.530.167.69
plot_mean_k0.280.000.28
plot_mean_var0.630.000.63
plot_ora4.860.115.01
plot_profile2.210.002.27
plot_qq0.850.030.87
plot_sample_tree1.120.001.13
read_gmt0.640.000.64
sample_annot000
sample_annotation0.030.010.05
save_plots0.050.000.04
select_genes0.280.000.28
show_plot0.240.000.24
write_files1.120.021.14

CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.050.040.08
adj_data0.590.000.60
cem0.030.000.03
cemitool17.25 0.1217.37
expr0000
expr_data0.250.000.25
filter_expr0.280.030.31
find_modules2.480.002.49
fit_data2.440.022.45
generate_report000
get_adj0.250.030.28
get_beta_data1.000.011.02
get_cemitool_r2_beta2.770.022.78
get_connectivity2.500.052.54
get_hubs0.030.010.05
get_merged_mods1.610.021.63
get_mods1.190.011.20
get_phi2.730.022.75
gsea_data4.590.034.62
interactions_data0.390.030.43
mod_colors0.040.000.03
mod_gene_num0.200.050.25
mod_gsea3.250.003.25
mod_names0.030.000.03
mod_ora3.640.123.76
mod_summary0.270.020.29
module_genes0.060.000.06
new_cem0.010.020.03
nmodules0.040.000.03
ora_data3.610.003.61
plot_beta_r20.230.000.23
plot_gsea4.330.004.33
plot_hist0.670.010.69
plot_interactions8.340.198.53
plot_mean_k0.280.000.28
plot_mean_var0.550.010.57
plot_ora5.240.145.37
plot_profile2.590.002.59
plot_qq0.580.000.58
plot_sample_tree1.170.001.17
read_gmt0.870.000.88
sample_annot0.020.000.01
sample_annotation0.020.000.02
save_plots0.030.000.03
select_genes0.300.000.29
show_plot0.140.000.14
write_files1.110.021.13