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BioC 3.6: CHECK report for scone on malbec1

This page was generated on 2017-08-16 13:25:18 -0400 (Wed, 16 Aug 2017).

Package 1213/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.1.2
Michael Cole
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scone
Last Changed Rev: 130908 / Revision: 131943
Last Changed Date: 2017-07-03 12:10:13 -0400 (Mon, 03 Jul 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: scone
Version: 1.1.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.1.2.tar.gz
StartedAt: 2017-08-16 02:17:46 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:24:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 392.1 seconds
RetCode: 0
Status:  OK 
CheckDir: scone.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck/00check.log’
for details.


scone.Rcheck/00install.out:

* 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)

scone.Rcheck/scone-Ex.timings:

nameusersystemelapsed
CLR_FN0.0000.0000.002
DESEQ_FN0.0000.0000.001
FQ_FN0.080.000.08
SCRAN_FN0.6080.0040.611
SUM_FN0.0000.0000.001
SconeExperiment-class0.3040.0000.305
TMM_FN0.0600.0000.061
UQ_FN0.0040.0000.002
biplot_color0.0080.0000.009
biplot_interactive0.5560.0040.788
control_genes0.0160.0000.018
estimate_ziber0.0400.0000.041
factor_sample_filter0.2400.0000.243
fast_estimate_ziber0.0320.0000.034
get_bio0.0280.0000.026
get_design0.4080.0000.408
get_negconruv0.0360.0000.034
get_normalized0.1600.0040.164
get_params0.0160.0000.014
get_qc0.0320.0000.034
get_scores0.0280.0000.028
impute_expectation0.0000.0000.001
impute_null000
lm_adjust0.0040.0000.004
make_design0.0000.0000.002
metric_sample_filter0.0040.0000.015
scone0.0920.0000.094
sconeReport0.0400.0000.039
scone_easybake0.0440.0000.042
score_matrix0.0040.0000.005
select_methods0.0360.0000.033
simple_FNR_params0.0240.0040.030