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CHECK report for CEMiTool on merida1

This page was generated on 2019-04-16 12:00:52 -0400 (Tue, 16 Apr 2019).

Package 224/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.6.11
Helder Nakaya
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_8
Last Commit: d4c4ae4
Last Changed Date: 2019-03-15 14:27:37 -0400 (Fri, 15 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 1.6.11
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_1.6.11.tar.gz
StartedAt: 2019-04-15 22:51:40 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:57:07 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 326.6 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_1.6.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CEMiTool.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.6.11’
* 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  6.6Mb
  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
cem_overlap : <anonymous>: no visible binding for global variable
  ‘splitBy’
cem_overlap: no visible binding for global variable ‘object’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘gene’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘P.Value’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘median’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘sd’
flip_vector: no visible global function definition for ‘setNames’
makeContMatrix: no visible global function definition for
  ‘model.matrix’
makeLimmaComp: no visible global function definition for ‘setNames’
mod_activity : <anonymous>: no visible binding for global variable
  ‘modules’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘gene’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘comparison’
mod_activity : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘logFC’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘module’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘fc_median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘parameter’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
  variable ‘value’
mod_activity : <anonymous>: no visible binding for global variable
  ‘new_col’
mod_activity : <anonymous>: no visible binding for global variable
  ‘comparison’
mod_activity : <anonymous>: no visible binding for global variable
  ‘parameter’
mod_activity : <anonymous>: no visible binding for global variable
  ‘value’
mod_activity : <anonymous>: no visible binding for global variable
  ‘module’
mod_compare : <anonymous>: no visible binding for global variable
  ‘modules’
mod_compare: no visible binding for global variable ‘first_mod’
mod_compare: no visible binding for global variable ‘second_mod’
mod_compare: no visible global function definition for ‘p.adjust’
mod_compare: no visible binding for global variable ‘Jaccard’
mod_compare: no visible binding for global variable ‘Fisherp’
mod_compare: no visible binding for global variable ‘fdr’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘value’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘pathway’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘module’
mod_info : <anonymous> : <anonymous>: no visible binding for global
  variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable
  ‘modules’
mod_info : <anonymous>: no visible binding for global variable ‘module’
mod_info: no visible binding for global variable ‘value’
mod_info: no visible binding for global variable ‘module’
plot_comembership: no visible binding for global variable ‘Var1’
plot_comembership: no visible binding for global variable ‘Freq’
plot_consensus: no visible global function definition for ‘sd’
plot_consensus: no visible binding for global variable ‘X1’
plot_consensus: no visible binding for global variable ‘Y1’
plot_consensus: no visible binding for global variable ‘X2’
plot_consensus: no visible binding for global variable ‘Y2’
plot_consensus: no visible binding for global variable ‘Communities’
plot_similarity: no visible binding for global variable ‘X1’
plot_similarity: no visible binding for global variable ‘Y1’
plot_similarity: no visible binding for global variable ‘X2’
plot_similarity: no visible binding for global variable ‘Y2’
plot_similarity: no visible binding for global variable ‘Weight’
plot_similarity: no visible binding for global variable ‘Names’
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.. := Communities Fisherp Freq Jaccard Mean
  Names P.Value Var1 Variance Weight X1 X2 Y1 Y2 as.dist comparison
  data dev.off dist fc_median fdr first_mod gene hclust head logFC
  median metric model.matrix module modules new_col num_genes object
  p.adjust parameter pathway sd second_mod setNames splitBy tail value
  var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "median",
             "model.matrix", "p.adjust", "sd", "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 or elapsed time > 5s
                    user system elapsed
cemitool          12.427  0.312  12.886
plot_interactions 11.641  0.216  12.191
plot_ora          10.695  0.126  10.983
mod_ora            9.878  0.727   9.828
ora_data           9.700  0.378   9.890
plot_gsea          5.681  2.303   4.445
mod_gsea           5.156  1.397   3.792
gsea_data          4.741  1.784   3.909
* 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-3.8-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/3.5/Resources/library’
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CEMiTool)

Tests output

CEMiTool.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 106 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 50.706  11.313  45.405 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0420.0040.046
adj_data0.5060.0280.535
cem0.4260.0060.438
cem_overlap0.0000.0000.001
cemitool12.427 0.31212.886
enrich_mods0.0000.0000.001
expr00.0010.0010.003
expr_data0.2340.0050.246
filter_expr0.2580.0090.269
find_modules1.8730.0431.943
fit_data1.9950.0412.049
generate_report000
get_adj0.1820.0130.198
get_beta_data0.6700.0130.690
get_cemitool_r2_beta1.9650.0482.040
get_connectivity1.9300.0471.998
get_hubs0.0250.0060.032
get_merged_mods1.0860.0261.125
get_mods0.9050.0160.928
get_phi2.0050.0402.059
gsea_data4.7411.7843.909
interactions_data0.8620.6740.537
makeContMatrix0.0000.0010.001
makeLimmaComp0.0010.0000.001
mod_colors0.0210.0050.027
mod_gene_num0.1680.0150.183
mod_gsea5.1561.3973.792
mod_names0.0790.0940.025
mod_ora9.8780.7279.828
mod_summary0.5750.0940.530
module_genes0.1250.1540.045
new_cem0.0800.1080.027
nmodules0.1700.2190.056
ora_data9.7000.3789.890
overlap_community000
plot_beta_r20.3070.0070.322
plot_comembership0.0000.0000.001
plot_consensus000
plot_gsea5.6812.3034.445
plot_hist0.7120.0080.725
plot_interactions11.641 0.21612.191
plot_mean_k0.3130.0090.325
plot_mean_var0.5540.0120.574
plot_ora10.695 0.12610.983
plot_profile3.0650.0293.118
plot_qq0.9090.0210.940
plot_sample_tree0.6130.0090.627
plot_similarity0.0000.0000.001
read_gmt0.7960.0120.812
sample_annot0.0030.0020.004
sample_annotation0.0190.0020.020
save_plots0.0370.0050.041
select_genes0.2410.0240.267
show_plot0.2080.0060.217
stat_overlap_mods000
write_files2.5921.9481.118