BioC 3.4: CHECK report for EGAD on morelia

Package: EGAD

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EGAD_1.1.4.tar.gz

StartedAt: 2016-09-20 06:00:03 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:03:17 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 193.8 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_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.1.4’
* 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 ... 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-3.4-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	0.002	0.000	0.002
auc_multifunc	0.002	0.000	0.001
auprc	0.003	0.000	0.003
auroc_analytic	0.001	0.000	0.001
build_binary_network	0.002	0.000	0.001
build_coexp_expressionSet	0.002	0.000	0.003
build_coexp_network	0.005	0.000	0.005
build_semantic_similarity_network	0.001	0.000	0.001
build_weighted_network	0	0	0
calculate_multifunc	0.003	0.000	0.002
conv_smoother	0.010	0.000	0.017
extend_network	0.002	0.000	0.003
filter_network	0.002	0.000	0.002
filter_network_cols	0.002	0.000	0.002
filter_network_rows	0.006	0.001	0.006
filter_orthologs	0.002	0.000	0.001
fmeasure	0.001	0.000	0.001
get_auc	0.002	0.000	0.002
get_counts	0.002	0.001	0.002
get_density	0.001	0.000	0.001
get_prc	0.000	0.000	0.001
get_roc	0.001	0.000	0.000
make_annotations	0.001	0.000	0.001
make_gene_network	0.001	0.000	0.001
make_genelist	0.001	0.000	0.001
neighbor_voting	0.025	0.002	0.027
node_degree	0.002	0.000	0.002
plot_densities	0.011	0.001	0.036
plot_density_compare	0.006	0.001	0.021
plot_distribution	0.005	0.000	0.009
plot_network_heatmap	0.025	0.004	0.207
plot_prc	0.010	0.001	0.028
plot_roc	0.002	0.000	0.010
plot_roc_overlay	0.135	0.004	0.277
predictions	0.028	0.000	0.028
repmat	0.001	0.000	0.001
run_GBA	0.012	0.000	0.013