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CHECK report for CEMiTool on merida2

This page was generated on 2019-04-09 13:35:29 -0400 (Tue, 09 Apr 2019).

Package 232/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.7.7
Helder Nakaya
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: master
Last Commit: d3739af
Last Changed Date: 2019-01-07 11:41:49 -0400 (Mon, 07 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: CEMiTool
Version: 1.7.7
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_1.7.7.tar.gz
StartedAt: 2019-04-08 23:46:21 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:51:08 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 286.7 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_1.7.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CEMiTool.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.7.7’
* 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_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’
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’
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 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
plot_interactions 9.397  0.173   9.626
cemitool          8.541  0.340   9.009
plot_gsea         6.155  2.641   4.525
mod_gsea          5.471  1.341   4.446
gsea_data         4.918  1.391   3.971
* 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-3.9-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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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: 94 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 45.599  11.309  39.933 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0220.0060.028
adj_data0.6020.0130.625
cem0.0270.0060.033
cem_overlap0.0010.0000.001
cemitool8.5410.3409.009
enrich_mods0.0000.0000.001
expr00.0010.0010.003
expr_data0.0380.0070.046
filter_expr0.3950.0180.416
find_modules1.3810.0221.436
fit_data1.1420.0161.170
generate_report0.0010.0000.000
get_adj0.2330.0100.247
get_beta_data0.9070.0320.960
get_cemitool_r2_beta1.4160.0231.453
get_connectivity1.2290.0211.268
get_hubs0.0180.0040.021
get_merged_mods0.8250.0140.847
get_mods0.7170.0070.730
get_phi1.2550.0171.285
gsea_data4.9181.3913.971
interactions_data0.9220.5660.528
makeContMatrix0.0010.0010.001
makeLimmaComp0.0000.0000.001
mod_colors0.0380.0120.051
mod_gsea5.4711.3414.446
mod_names0.0980.0910.027
mod_ora4.3000.6104.125
mod_summary0.1120.0650.072
module_genes0.0970.0990.047
new_cem0.0680.0500.027
nmodules0.1050.0950.049
ora_data3.3070.2053.336
overlap_community0.0000.0000.001
plot_beta_r20.2150.0060.223
plot_comembership0.0000.0000.001
plot_consensus000
plot_gsea6.1552.6414.525
plot_hist0.4720.0470.528
plot_interactions9.3970.1739.626
plot_mean_k0.2270.0060.234
plot_mean_var0.6230.0460.674
plot_ora3.8570.1564.048
plot_profile2.2020.0172.239
plot_qq2.5650.2962.885
plot_sample_tree0.7370.0370.782
plot_similarity0.0010.0000.001
read_gmt0.9190.0260.951
sample_annot0.0030.0020.005
sample_annotation0.0190.0020.021
save_plots0.0350.0060.042
show_plot0.2280.0060.234
stat_overlap_mods0.0010.0000.001
write_files0.5640.4470.215