BioC 3.3: CHECK report for EGAD on oaxaca

Package: EGAD

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EGAD_1.0.4.tar.gz

StartedAt: 2016-10-13 01:10:16 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:14:57 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 281.3 seconds

RetCode: 0

Status:  OK

CheckDir: EGAD.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EGAD_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/EGAD.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.4’
* 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 ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/EGAD.Rcheck/00check.log’
for details.

* installing *source* package ‘EGAD’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
* DONE (EGAD)

name	user	system	elapsed
assortativity	0.003	0.000	0.003
auc_multifunc	0.003	0.000	0.002
auprc	0.004	0.000	0.005
auroc_analytic	0.001	0.000	0.002
build_binary_network	0.001	0.000	0.001
build_coexp_expressionSet	0.015	0.000	0.016
build_coexp_network	0.008	0.000	0.008
build_semantic_similarity_network	0.001	0.000	0.001
build_weighted_network	0.000	0.000	0.001
calculate_multifunc	0.004	0.001	0.003
conv_smoother	0.014	0.000	0.014
extend_network	0.004	0.000	0.005
filter_network	0.002	0.000	0.002
filter_network_cols	0.003	0.001	0.003
filter_network_rows	0.003	0.001	0.003
filter_orthologs	0.002	0.000	0.002
fmeasure	0.001	0.000	0.001
get_auc	0.003	0.000	0.003
get_counts	0.003	0.000	0.003
get_density	0.002	0.000	0.002
get_prc	0.000	0.000	0.001
get_roc	0.001	0.000	0.001
make_annotations	0.001	0.000	0.002
make_gene_network	0.001	0.000	0.002
make_genelist	0.000	0.000	0.001
neighbor_voting	0.040	0.002	0.042
node_degree	0.001	0.000	0.002
plot_densities	0.011	0.001	0.012
plot_density_compare	0.007	0.001	0.008
plot_distribution	0.006	0.001	0.006
plot_network_heatmap	0.043	0.002	0.045
plot_prc	0.012	0.002	0.016
plot_roc	0.002	0.000	0.002
plot_roc_overlay	0.197	0.004	0.306
predictions	0.011	0.000	0.011
repmat	0.030	0.001	0.031
run_GBA	0.022	0.001	0.023