BioC experimental data: CHECK report for Mulder2012 on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/Mulder2012.Rcheck’
* using R version 3.4.2 (2017年09月28日)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mulder2012/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulder2012’ version ‘0.16.0’
* 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 ‘Mulder2012’ can be installed ... OK
* checking installed package size ... NOTE
 installed size is 22.4Mb
 sub-directories of 1Mb or more:
 data 19.9Mb
 doc 2.4Mb
* 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' call to ‘snow’ in package code.
 Please use :: or requireNamespace() instead.
 See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘MASS’
 All declared Imports should be used.
Packages in Depends field not imported from:
 ‘KEGG.db’ ‘org.Hs.eg.db’
 These packages need to be imported from (in the NAMESPACE file)
 for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Arora2010.BMfitting: no visible global function definition for ‘new’
Arora2010.InferPAN: no visible global function definition for ‘new’
Arora2010.fig: no visible global function definition for ‘data’
Arora2010.fig: no visible global function definition for ‘pdf’
Arora2010.fig: no visible binding for global variable ‘bm_Arora2010’
Arora2010.fig: no visible global function definition for ‘graphics.off’
Arora2010.fig: no visible binding for global variable ‘pan_Arora2010’
Arora2010.fig: no visible global function definition for ‘par’
Arora2010.fig: no visible global function definition for ‘barplot’
Arora2010.hypergeo : Arora2010.pathway: no visible global function
 definition for ‘p.adjust’
Arora2010.hypergeo : Arora2010.pathway: no visible binding for global
 variable ‘KEGGPATHID2NAME’
Arora2010.pipeline: no visible global function definition for ‘data’
Arora2010.pipeline: no visible binding for global variable ‘Arora2010’
GSEARandomWalkFig: no visible global function definition for ‘par’
Mulder2012.BMfitting: no visible global function definition for ‘new’
Mulder2012.BMfitting.extended: no visible global function definition
 for ‘new’
Mulder2012.InferPAN: no visible global function definition for ‘new’
Mulder2012.PPIPre: no visible global function definition for ‘data’
Mulder2012.PPIPre: no visible binding for global variable
 ‘PINdbProteins’
Mulder2012.PPIPre : <anonymous>: no visible binding for global variable
 ‘PINdbProteins’
Mulder2012.RNAiPre: no visible global function definition for ‘sd’
Mulder2012.fig: no visible global function definition for ‘data’
Mulder2012.fig: no visible global function definition for ‘pdf’
Mulder2012.fig: no visible binding for global variable ‘bm_Mulder2012’
Mulder2012.fig: no visible global function definition for
 ‘graphics.off’
Mulder2012.fig: no visible binding for global variable ‘Mulder2012’
Mulder2012.fig: no visible binding for global variable ‘PPI’
Mulder2012.fig: no visible binding for global variable
 ‘bm_ext_Mulder2012’
Mulder2012.fig: no visible binding for global variable
 ‘pan_ext_Mulder2012’
dist.pvclust4PAN: no visible global function definition for ‘as.dist’
dist.pvclust4PAN: no visible global function definition for ‘cor’
dist.pvclust4PAN: no visible global function definition for ‘na.omit’
dist.pvclust4PAN: no visible global function definition for ‘dist’
parPvclust4PAN: no visible global function definition for ‘parLapply’
parPvclust4PAN: no visible global function definition for
 ‘getFromNamespace’
parPvclust4PAN: no visible global function definition for ‘hclust’
Undefined global functions or variables:
 Arora2010 KEGGPATHID2NAME Mulder2012 PINdbProteins PPI as.dist
 barplot bm_Arora2010 bm_Mulder2012 bm_ext_Mulder2012 cor data dist
 getFromNamespace graphics.off hclust na.omit new p.adjust
 pan_Arora2010 pan_ext_Mulder2012 par parLapply pdf sd
Consider adding
 importFrom("grDevices", "graphics.off", "pdf")
 importFrom("graphics", "barplot", "par")
 importFrom("methods", "new")
 importFrom("stats", "as.dist", "cor", "dist", "hclust", "na.omit",
 "p.adjust", "sd")
 importFrom("utils", "data", "getFromNamespace")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
 ‘/home/biocbuild/bbs-3.5-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.

* installing *source* package ‘Mulder2012’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (Mulder2012)