Package: Mulder2012

Version: 0.24.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Mulder2012.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Mulder2012_0.24.0.tar.gz

StartedAt: 2019-10-17 13:33:26 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:35:36 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 130.3 seconds

RetCode: 0

Status:  OK

CheckDir: Mulder2012.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Mulder2012.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Mulder2012_0.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/Mulder2012.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘0.24.0’
* 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 20.1Mb
  sub-directories of 1Mb or more:
    data  19.9Mb
* 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 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 : : 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 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-3.9-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Mulder2012
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Mulder2012’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** testing if installed package keeps a record of temporary installation path
* DONE (Mulder2012)

name	user	system	elapsed
Arora2010.BMfitting	0	0	0
Arora2010.InferPAN	0	0	0
Arora2010.ModuleSearchByPvclust	0	0	0
Arora2010.fig	0	0	0
Arora2010.hypergeo	0	0	0
Arora2010.module.visualize	0	0	0
Arora2010.pipeline	0.000	0.000	0.001
GSEARandomWalkFig	0	0	0
Mulder2012.BMfitting	0	0	0
Mulder2012.InferPAN	0	0	0
Mulder2012.ModuleSearchByPvclust	0	0	0
Mulder2012.PPIPre	0	0	0
Mulder2012.PPIenrich	0	0	0
Mulder2012.RNAiPre	0.000	0.000	0.001
Mulder2012.fig	0	0	0
Mulder2012.module.visualize	0	0	0
Mulder2012.pipeline	0	0	0
data-Arora2010	1.022	0.004	1.026
data-Mulder2012	0.466	0.008	0.474