BioC 3.3: CHECK report for EGAD on moscato2

Package: EGAD

Version: 1.0.4

Command: rm -rf EGAD.buildbin-libdir EGAD.Rcheck && mkdir EGAD.buildbin-libdir EGAD.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGAD.buildbin-libdir EGAD_1.0.4.tar.gz >EGAD.Rcheck\00install.out 2>&1 && cp EGAD.Rcheck\00install.out EGAD-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=EGAD.buildbin-libdir --install="check:EGAD-install.out" --force-multiarch --no-vignettes --timings EGAD_1.0.4.tar.gz

StartedAt: 2016-10-13 03:24:10 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:31:29 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 439.1 seconds

RetCode: 0

Status:  OK

CheckDir: EGAD.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EGAD.buildbin-libdir EGAD.Rcheck && mkdir EGAD.buildbin-libdir EGAD.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGAD.buildbin-libdir EGAD_1.0.4.tar.gz >EGAD.Rcheck\00install.out 2>&1 && cp EGAD.Rcheck\00install.out EGAD-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=EGAD.buildbin-libdir --install="check:EGAD-install.out" --force-multiarch --no-vignettes --timings EGAD_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/EGAD.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'EGAD' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 42.3Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/EGAD.Rcheck/00check.log'
for details.

install for i386

* 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'

install for x64

* installing *source* package 'EGAD' ...
** 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'
* MD5 sums
packaged installation of 'EGAD' as EGAD_1.0.4.zip
* DONE (EGAD)

name	user	system	elapsed
assortativity	0.00	0.02	0.01
auc_multifunc	0	0	0
auprc	0	0	0
auroc_analytic	0	0	0
build_binary_network	0	0	0
build_coexp_expressionSet	0.03	0.00	0.03
build_coexp_network	0	0	0
build_semantic_similarity_network	0.02	0.00	0.02
build_weighted_network	0	0	0
calculate_multifunc	0	0	0
conv_smoother	0.01	0.00	0.01
extend_network	0	0	0
filter_network	0	0	0
filter_network_cols	0.28	0.00	0.28
filter_network_rows	0	0	0
filter_orthologs	0	0	0
fmeasure	0	0	0
get_auc	0	0	0
get_counts	0	0	0
get_density	0	0	0
get_prc	0	0	0
get_roc	0.02	0.00	0.01
make_annotations	0	0	0
make_gene_network	0	0	0
make_genelist	0	0	0
neighbor_voting	0.03	0.00	0.04
node_degree	0	0	0
plot_densities	0.01	0.00	0.02
plot_density_compare	0.02	0.00	0.01
plot_distribution	0	0	0
plot_network_heatmap	0.07	0.00	0.08
plot_prc	0.02	0.00	0.02
plot_roc	0	0	0
plot_roc_overlay	0.22	0.01	0.23
predictions	0.01	0.00	0.02
repmat	0	0	0
run_GBA	0.04	0.00	0.03

name	user	system	elapsed
assortativity	0.01	0.00	0.01
auc_multifunc	0	0	0
auprc	0.02	0.00	0.02
auroc_analytic	0	0	0
build_binary_network	0	0	0
build_coexp_expressionSet	0.01	0.00	0.01
build_coexp_network	0.02	0.00	0.02
build_semantic_similarity_network	0	0	0
build_weighted_network	0	0	0
calculate_multifunc	0.05	0.00	0.04
conv_smoother	0.03	0.00	0.04
extend_network	0.01	0.00	0.01
filter_network	0	0	0
filter_network_cols	0.02	0.00	0.02
filter_network_rows	0	0	0
filter_orthologs	0	0	0
fmeasure	0.02	0.00	0.01
get_auc	0	0	0
get_counts	0	0	0
get_density	0	0	0
get_prc	0	0	0
get_roc	0	0	0
make_annotations	0	0	0
make_gene_network	0	0	0
make_genelist	0	0	0
neighbor_voting	0.64	0.00	0.64
node_degree	0	0	0
plot_densities	0.02	0.00	0.01
plot_density_compare	0.01	0.00	0.02
plot_distribution	0.02	0.00	0.02
plot_network_heatmap	0.09	0.00	0.09
plot_prc	0.03	0.00	0.03
plot_roc	0	0	0
plot_roc_overlay	0.39	0.01	0.41
predictions	0.01	0.00	0.02
repmat	0	0	0
run_GBA	0.04	0.00	0.03