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CHECK report for EGAD on veracruz1

This page was generated on 2018-04-12 13:42:58 -0400 (Thu, 12 Apr 2018).

Package 412/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.6.0
Sara Ballouz
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/EGAD
Branch: RELEASE_3_6
Last Commit: 0f0749f
Last Changed Date: 2017-10-30 12:41:17 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EGAD
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EGAD_1.6.0.tar.gz
StartedAt: 2018-04-12 03:14:03 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:17:37 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 214.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EGAD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EGAD_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/EGAD.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 42.2Mb
  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 loading without being on the library search path ... 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 ‘rgb’
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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/EGAD.Rcheck/00check.log’
for details.



Installation output

EGAD.Rcheck/00install.out

* installing *source* package ‘EGAD’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EGAD)

Tests output

EGAD.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
  8.067   0.287   8.755 

Example timings

EGAD.Rcheck/EGAD-Ex.timings

nameusersystemelapsed
assortativity0.0030.0000.003
auc_multifunc0.0020.0010.002
auprc0.0600.0020.063
auroc_analytic0.0010.0000.001
build_binary_network0.0020.0000.001
build_coexp_expressionSet0.0040.0010.005
build_coexp_network0.0070.0010.010
build_semantic_similarity_network0.0020.0000.002
build_weighted_network0.0010.0000.002
calculate_multifunc0.0040.0000.004
conv_smoother0.0110.0010.012
extend_network0.0020.0000.002
filter_network0.0030.0000.002
filter_network_cols0.0140.0000.014
filter_network_rows0.0030.0000.003
filter_orthologs0.0020.0000.002
fmeasure0.0120.0000.012
get_auc0.2130.0010.218
get_counts0.0030.0000.005
get_density0.0020.0000.002
get_prc0.0010.0000.001
get_roc0.0010.0000.001
make_annotations0.0020.0000.002
make_gene_network0.0020.0000.002
make_genelist0.0020.0000.002
neighbor_voting0.1590.0020.169
node_degree0.0010.0010.001
plot_densities0.0210.0010.021
plot_density_compare0.0110.0010.013
plot_distribution0.0040.0000.005
plot_network_heatmap0.0270.0020.030
plot_prc0.0110.0010.013
plot_roc0.0010.0000.002
plot_roc_overlay0.1930.0050.204
predictions0.0070.0010.007
repmat0.0010.0000.001
run_GBA0.0420.0010.046