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CHECK report for CEMiTool on tokay2

This page was generated on 2018-10-17 08:44:20 -0400 (Wed, 17 Oct 2018).

Package 209/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.4.2
Helder Nakaya
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_7
Last Commit: 91964b6
Last Changed Date: 2018-06-25 14:17:49 -0400 (Mon, 25 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CEMiTool
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CEMiTool_1.4.2.tar.gz
StartedAt: 2018-10-17 00:59:29 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:08:05 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 516.6 seconds
RetCode: 0
Status:  OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CEMiTool_1.4.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CEMiTool.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.4.2'
* 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 ... 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
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mod_ora              10.50   0.12   10.63
ora_data              9.72   0.06    9.78
plot_interactions     9.26   0.13    9.39
plot_ora              8.61   0.02    8.62
fit_data              5.27   0.02    5.28
get_cemitool_r2_beta  5.15   0.00    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ora_data          9.45   0.01    9.47
plot_ora          8.53   0.02    8.55
mod_ora           7.74   0.07    7.80
plot_interactions 7.66   0.13    7.78
find_modules      6.06   0.01    6.08
gsea_data         3.41   0.03   21.62
* 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-3.7-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.



Installation output

CEMiTool.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CEMiTool_1.4.2.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.4.2.zip && rm CEMiTool_1.4.2.tar.gz CEMiTool_1.4.2.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  33.1M      0 --:--:-- --:--:-- --:--:-- 34.9M

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  
    expr0                                   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  
    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  
    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_1.4.2.zip
* DONE (CEMiTool)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

CEMiTool.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  35.53    1.71   37.20 

CEMiTool.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  46.62    1.53   48.14 

Example timings

CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.060.030.09
adj_data0.270.000.36
cem0.030.020.05
cem_overlap000
cemitool000
expr00.000.010.02
expr_data0.040.000.04
filter_expr0.470.000.47
find_modules4.550.084.67
fit_data5.270.025.28
generate_report000
geom_qq000
get_adj0.210.010.24
get_beta_data1.930.001.92
get_cemitool_r2_beta5.150.005.16
get_connectivity4.360.024.37
get_hubs0.030.000.03
get_merged_mods2.500.032.53
get_mods0.640.020.66
get_phi4.300.014.31
gsea_data3.690.244.02
interactions_data0.500.060.56
mod_colors0.030.000.03
mod_gsea4.370.004.37
mod_names0.030.000.03
mod_ora10.50 0.1210.63
mod_summary0.100.000.09
module_genes0.040.000.05
new_cem0.020.020.03
nmodules0.140.000.14
ora_data9.720.069.78
plot_beta_r20.400.021.33
plot_gsea4.330.014.34
plot_hist0.600.030.63
plot_interactions9.260.139.39
plot_mean_k0.220.000.22
plot_mean_var0.50.00.5
plot_ora8.610.028.62
plot_profile2.050.002.05
plot_qq3.210.093.31
plot_sample_tree0.750.080.97
read_gmt1.040.001.03
sample_annot000
sample_annotation0.010.000.02
save_plots0.050.000.05
show_plot0.170.010.18
write_files000

CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.030.010.04
adj_data0.310.030.35
cem0.020.030.05
cem_overlap000
cemitool0.020.000.01
expr0000
expr_data0.030.030.07
filter_expr0.640.050.68
find_modules6.060.016.08
fit_data4.230.004.24
generate_report000
geom_qq000
get_adj0.140.000.14
get_beta_data2.150.072.20
get_cemitool_r2_beta4.310.004.31
get_connectivity4.690.014.71
get_hubs0.030.000.03
get_merged_mods2.420.002.42
get_mods0.670.000.67
get_phi4.250.024.27
gsea_data 3.41 0.0321.62
interactions_data0.350.010.36
mod_colors0.010.020.03
mod_gsea2.810.012.83
mod_names0.050.000.04
mod_ora7.740.077.80
mod_summary0.040.000.05
module_genes0.050.010.06
new_cem0.010.020.03
nmodules0.070.000.06
ora_data9.450.019.47
plot_beta_r20.220.020.24
plot_gsea3.120.003.12
plot_hist0.660.060.72
plot_interactions7.660.137.78
plot_mean_k0.200.010.22
plot_mean_var0.530.000.53
plot_ora8.530.028.55
plot_profile2.580.012.59
plot_qq3.780.244.02
plot_sample_tree0.670.030.70
read_gmt0.470.020.48
sample_annot000
sample_annotation0.010.000.02
save_plots0.070.000.06
show_plot0.250.000.25
write_files000