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CHECK report for CEMiTool on tokay1

This page was generated on 2020-04-15 12:28:49 -0400 (Wed, 15 Apr 2020).

Package 251/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.10.2
Helder Nakaya
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_10
Last Commit: b2830d1
Last Changed Date: 2020-03-27 11:45:16 -0400 (Fri, 27 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CEMiTool
Version: 1.10.2
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CEMiTool_1.10.2.tar.gz
StartedAt: 2020-04-15 01:56:22 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:03:26 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 423.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CEMiTool_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CEMiTool.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.10.2'
* 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  6.7Mb
  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
  '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_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 '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 data dev.off dist
  hclust head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "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
cemitool          10.46   0.17   10.69
plot_interactions  9.12   0.13    9.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
cemitool          10.79   0.08   10.97
plot_interactions  8.49   0.08    8.57
* 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-3.10-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/3.10/bioc/src/contrib/CEMiTool_1.10.2.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.10.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.10.2.zip && rm CEMiTool_1.10.2.tar.gz CEMiTool_1.10.2.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
 19 4046k   19  784k    0     0  3863k      0  0:00:01 --:--:--  0:00:01 3920k
100 4046k  100 4046k    0     0  13.8M      0 --:--:-- --:--:-- --:--:-- 14.0M

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_1.10.2.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked

Tests output

CEMiTool.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  35.17    1.65   36.78 

CEMiTool.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  41.26    0.79   41.92 

Example timings

CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.020.020.03
adj_data0.280.030.31
cem0.040.000.03
cemitool10.46 0.1710.69
expr0000
expr_data0.240.000.23
filter_expr0.200.010.22
find_modules1.940.021.97
fit_data1.640.001.64
generate_report000
get_adj0.140.000.14
get_beta_data0.770.000.76
get_cemitool_r2_beta1.900.021.93
get_connectivity2.050.002.05
get_hubs0.050.000.05
get_merged_mods0.790.000.79
get_mods0.690.030.72
get_phi1.500.001.52
gsea_data3.530.053.57
interactions_data0.300.000.54
mod_colors0.030.000.03
mod_gene_num0.060.000.06
mod_gsea2.880.062.91
mod_names0.030.020.04
mod_ora3.090.063.16
mod_summary0.640.030.67
module_genes0.050.000.05
new_cem0.050.000.04
nmodules0.030.000.04
ora_data2.690.012.70
plot_beta_r20.140.000.15
plot_gsea2.920.002.92
plot_hist0.440.000.43
plot_interactions9.120.139.25
plot_mean_k0.160.010.18
plot_mean_var0.420.030.45
plot_ora3.000.223.22
plot_profile1.830.001.83
plot_qq0.450.020.47
plot_sample_tree0.560.010.57
read_gmt0.50.00.5
sample_annot0.020.000.02
sample_annotation0.010.020.03
save_plots0.040.000.03
select_genes0.560.020.58
show_plot0.140.000.14
write_files0.580.010.59

CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.010.000.02
adj_data0.440.030.47
cem0.020.010.03
cemitool10.79 0.0810.97
expr0000
expr_data0.150.000.16
filter_expr0.190.000.19
find_modules1.850.001.86
fit_data1.860.001.86
generate_report000
get_adj0.210.020.23
get_beta_data1.020.001.02
get_cemitool_r2_beta2.440.012.45
get_connectivity2.180.002.19
get_hubs0.040.000.03
get_merged_mods1.310.021.33
get_mods1.050.001.04
get_phi2.550.002.56
gsea_data4.360.014.33
interactions_data0.450.020.47
mod_colors0.020.010.03
mod_gene_num0.090.020.11
mod_gsea3.590.033.62
mod_names0.030.000.03
mod_ora3.550.003.55
mod_summary0.740.030.75
module_genes0.030.000.03
new_cem0.010.000.02
nmodules0.020.000.01
ora_data2.780.022.80
plot_beta_r20.280.000.28
plot_gsea3.000.013.02
plot_hist0.750.020.76
plot_interactions8.490.088.57
plot_mean_k0.20.00.2
plot_mean_var0.370.040.42
plot_ora4.050.024.06
plot_profile2.360.002.36
plot_qq0.470.000.47
plot_sample_tree0.870.000.88
read_gmt0.780.000.78
sample_annot000
sample_annotation0.020.010.03
save_plots0.030.000.04
select_genes0.380.000.37
show_plot0.230.000.25
write_files1.080.031.09