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CHECK report for CEMiTool on merida1

This page was generated on 2020-08-11 12:00:47 -0400 (Tue, 11 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: 2020-08-10 14:50:56 -0400 (Mon, 10 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  NA 
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.13.1.tar.gz
StartedAt: 2020-08-11 03:20:47 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 03:26:19 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 331.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.13.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CEMiTool.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CEMiTool’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
cemitool          13.719  0.277  14.013
plot_interactions  9.903  0.182  10.120
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.



Installation output

CEMiTool.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CEMiTool
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (CEMiTool)

Tests output

CEMiTool.Rcheck/tests/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-apple-darwin17.0 (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 
 41.679   1.104  42.829 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0540.0060.059
adj_data0.5070.0230.530
cem0.4430.0100.454
cemitool13.719 0.27714.013
expr00.0000.0010.002
expr_data0.1790.0080.186
filter_expr0.2770.0090.286
find_modules2.2020.0222.227
fit_data2.2510.0262.281
generate_report000
get_adj0.2440.0090.253
get_beta_data0.7860.0100.797
get_cemitool_r2_beta2.2110.0202.235
get_connectivity2.1390.0222.163
get_hubs0.0280.0020.031
get_merged_mods1.2250.0141.240
get_mods0.9130.0090.922
get_phi2.1280.0192.150
gsea_data4.3410.0604.407
interactions_data0.3520.0260.380
mod_colors0.0220.0020.023
mod_gene_num0.1410.0070.147
mod_gsea3.6060.0323.645
mod_names0.0300.0050.035
mod_ora3.9180.0623.987
mod_summary0.2920.0060.298
module_genes0.0550.0110.065
new_cem0.0210.0030.024
nmodules0.0290.0040.033
ora_data4.1110.0664.181
plot_beta_r20.2230.0040.226
plot_gsea4.0580.0244.087
plot_hist0.6550.0100.666
plot_interactions 9.903 0.18210.120
plot_mean_k0.2630.0040.266
plot_mean_var0.6120.0190.631
plot_ora4.5140.0714.854
plot_profile2.5720.0342.614
plot_qq0.5080.0230.532
plot_sample_tree1.0910.0131.109
read_gmt1.0980.0071.107
sample_annot0.0030.0030.006
sample_annotation0.0270.0050.032
save_plots0.0440.0020.047
select_genes0.3110.0120.323
show_plot0.2180.0080.228
write_files0.9810.0221.004