BioC 3.6: CHECK report for scone on veracruz1

Package: scone

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scone_1.1.2.tar.gz

StartedAt: 2017-08-16 08:19:38 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:27:43 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 484.7 seconds

RetCode: 0

Status:  OK

CheckDir: scone.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scone_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.1.2’
* 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 ‘scone’ can be installed ... OK
* checking installed package size ... OK
* 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
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plotly’ ‘visNetwork’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘shiny::renderPlotly’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sconeReport: no visible global function definition for
  ‘visNetworkOutput’
sconeReport: no visible global function definition for ‘plotlyOutput’
sconeReport : server: no visible global function definition for
  ‘renderVisNetwork’
sconeReport : server: no visible global function definition for ‘%>%’
sconeReport : server: no visible global function definition for
  ‘visNetwork’
sconeReport : server: no visible global function definition for
  ‘visHierarchicalLayout’
sconeReport : server: no visible global function definition for
  ‘visGroups’
sconeReport : server: no visible global function definition for
  ‘visEdges’
sconeReport : server: no visible global function definition for
  ‘visOptions’
sconeReport : server: no visible global function definition for
  ‘visLegend’
sconeReport : server: no visible global function definition for
  ‘visNetworkProxy’
sconeReport : server: no visible global function definition for
  ‘visSelectNodes’
sconeReport : server: no visible global function definition for
  ‘setNames’
sconeReport : server: no visible global function definition for
  ‘plot_ly’
sconeReport : server: no visible global function definition for
  ‘ggplot’
sconeReport : server: no visible global function definition for ‘aes’
sconeReport : server: no visible global function definition for
  ‘geom_bar’
sconeReport : server: no visible global function definition for ‘ylim’
sconeReport : server: no visible global function definition for ‘labs’
sconeReport : server: no visible global function definition for ‘theme’
sconeReport : server: no visible global function definition for
  ‘element_blank’
sconeReport : server: no visible global function definition for
  ‘ggplotly’
sconeReport : server: no visible global function definition for
  ‘geom_violin’
sconeReport : server: no visible global function definition for
  ‘coord_cartesian’
sconeReport : server: no visible global function definition for
  ‘scale_fill_manual’
sconeReport : server: no visible global function definition for
  ‘geom_point’
sconeReport : server: no visible global function definition for
  ‘guides’
sconeReport : server: no visible binding for global variable ‘var’
sconeReport : server: no visible global function definition for
  ‘boxplot’
sconeReport : server : <anonymous>: no visible global function
  definition for ‘write.csv’
score_matrix: no visible global function definition for ‘var’
Undefined global functions or variables:
  %>% aes boxplot coord_cartesian element_blank geom_bar geom_point
  geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput
  renderVisNetwork scale_fill_manual setNames theme var visEdges
  visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput
  visNetworkProxy visOptions visSelectNodes write.csv ylim
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "setNames", "var")
  importFrom("utils", "write.csv")
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 ... 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-3.6-bioc/meat/scone.Rcheck/00check.log’
for details.

* installing *source* package ‘scone’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scone)

name	user	system	elapsed
CLR_FN	0.002	0.000	0.002
DESEQ_FN	0.002	0.001	0.002
FQ_FN	0.118	0.002	0.124
SCRAN_FN	0.802	0.024	0.847
SUM_FN	0.000	0.000	0.001
SconeExperiment-class	0.448	0.005	0.461
TMM_FN	0.098	0.001	0.102
UQ_FN	0.002	0.000	0.002
biplot_color	0.012	0.001	0.013
biplot_interactive	0.742	0.005	0.766
control_genes	0.020	0.010	0.031
estimate_ziber	0.058	0.001	0.059
factor_sample_filter	0.348	0.005	0.356
fast_estimate_ziber	0.048	0.000	0.048
get_bio	0.030	0.000	0.031
get_design	0.479	0.002	0.485
get_negconruv	0.048	0.001	0.047
get_normalized	0.224	0.001	0.231
get_params	0.014	0.000	0.013
get_qc	0.044	0.001	0.047
get_scores	0.042	0.001	0.044
impute_expectation	0.002	0.000	0.003
impute_null	0.001	0.000	0.001
lm_adjust	0.005	0.000	0.006
make_design	0.002	0.000	0.003
metric_sample_filter	0.008	0.001	0.010
scone	0.127	0.002	0.129
sconeReport	0.056	0.001	0.058
scone_easybake	0.051	0.001	0.056
score_matrix	0.006	0.000	0.006
select_methods	0.045	0.000	0.045
simple_FNR_params	0.037	0.001	0.042