Package: EGAD

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EGAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EGAD_1.8.0.tar.gz

StartedAt: 2018-10-16 21:08:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:12:38 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 223.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: EGAD.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EGAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EGAD_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/EGAD.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.8.0’
* 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 ‘EGAD’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 41.4Mb
  sub-directories of 1Mb or more:
    data  41.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘affy’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assortativity: no visible global function definition for ‘cor’
build_coexp_network: no visible global function definition for ‘cor’
conv_smoother: no visible global function definition for ‘convolve’
conv_smoother: no visible global function definition for ‘plot’
conv_smoother: no visible global function definition for ‘polygon’
conv_smoother: no visible global function definition for ‘points’
conv_smoother: no visible global function definition for ‘lines’
get_biogrid: no visible global function definition for ‘download.file’
get_biogrid: no visible global function definition for ‘unzip’
get_biogrid: no visible global function definition for ‘read.table’
get_expression_data_gemma: no visible global function definition for
  ‘read.table’
get_expression_matrix_from_GEO: no visible global function definition
  for ‘median’
get_expression_matrix_from_GEO: no visible global function definition
  for ‘aggregate’
get_expression_matrix_from_GEO: no visible binding for global variable
  ‘median’
get_phenocarta: no visible global function definition for ‘read.table’
make_transparent: no visible global function definition for ‘col2rgb’
make_transparent : <anonymous>: no visible global function definition
  for ‘rgb’
plot_densities: no visible global function definition for ‘plot’
plot_densities : <anonymous>: no visible global function definition for
  ‘polygon’
plot_densities : <anonymous>: no visible global function definition for
  ‘lines’
plot_density_compare: no visible global function definition for
  ‘density’
plot_density_compare: no visible global function definition for ‘plot’
plot_density_compare: no visible global function definition for
  ‘polygon’
plot_density_compare: no visible global function definition for ‘lines’
plot_distribution: no visible global function definition for ‘hist’
plot_distribution: no visible global function definition for ‘boxplot’
plot_distribution: no visible global function definition for ‘plot’
plot_distribution: no visible global function definition for ‘polygon’
plot_distribution: no visible global function definition for ‘lines’
plot_distribution: no visible global function definition for ‘abline’
plot_prc: no visible global function definition for ‘plot’
plot_prc: no visible global function definition for ‘abline’
plot_roc: no visible global function definition for ‘plot’
plot_roc_overlay: no visible global function definition for ‘axis’
plot_roc_overlay: no visible global function definition for ‘lines’
plot_value_compare: no visible global function definition for ‘plot’
plot_value_compare: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate axis boxplot col2rgb convolve cor density
  download.file hist lines median plot points polygon read.table rgb
  unzip
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "lines",
             "plot", "points", "polygon")
  importFrom("stats", "aggregate", "convolve", "cor", "density",
             "median")
  importFrom("utils", "download.file", "read.table", "unzip")
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 ... WARNING
Codoc mismatches from documentation object 'conv_smoother':
conv_smoother
  Code: function(X, Y, window, raw = FALSE, output = FALSE, ...)
  Docs: function(X, Y, window, xlab = "", ylab = "", raw = FALSE)
  Argument names in code not in docs:
    output ...
  Argument names in docs not in code:
    xlab ylab
  Mismatches in argument names:
    Position: 4 Code: raw Docs: xlab
    Position: 5 Code: output Docs: ylab
    Position: 6 Code: ... Docs: raw

* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/EGAD.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EGAD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘EGAD’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (EGAD)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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(EGAD)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("EGAD")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  8.852   0.491  10.000 

name	user	system	elapsed
assortativity	0.003	0.000	0.003
auc_multifunc	0.002	0.001	0.003
auprc	0.008	0.001	0.008
auroc_analytic	0.001	0.000	0.002
build_binary_network	0.002	0.000	0.002
build_coexp_expressionSet	0.005	0.001	0.006
build_coexp_network	0.006	0.000	0.007
build_semantic_similarity_network	0.002	0.000	0.002
build_weighted_network	0.001	0.000	0.002
calculate_multifunc	0.004	0.000	0.004
conv_smoother	0.010	0.000	0.011
extend_network	0.003	0.000	0.004
filter_network	0.002	0.000	0.002
filter_network_cols	0.006	0.001	0.006
filter_network_rows	0.003	0.000	0.004
filter_orthologs	0.002	0.001	0.003
fmeasure	0.002	0.000	0.002
get_auc	0.002	0.000	0.003
get_counts	0.005	0.000	0.004
get_density	0.002	0.000	0.001
get_prc	0.002	0.001	0.002
get_roc	0.002	0.000	0.001
make_annotations	0.002	0.000	0.002
make_gene_network	0.475	0.001	0.483
make_genelist	0.002	0.000	0.002
neighbor_voting	0.038	0.002	0.040
node_degree	0.003	0.000	0.003
plot_densities	0.029	0.000	0.029
plot_density_compare	0.011	0.000	0.012
plot_distribution	0.008	0.000	0.008
plot_network_heatmap	0.031	0.002	0.033
plot_prc	0.016	0.001	0.017
plot_roc	0.003	0.000	0.004
plot_roc_overlay	0.076	0.006	0.083
predictions	0.009	0.001	0.010
repmat	0.001	0.000	0.001
run_GBA	0.018	0.001	0.020