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BioC experimental data: CHECK report for Mulder2012 on zin2

This page was generated on 2016-10-08 19:29:22 -0700 (Sat, 08 Oct 2016).

Package 190/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mulder2012 0.12.0
Xin Wang
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/Mulder2012
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 

Summary

Package: Mulder2012
Version: 0.12.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.12.0.tar.gz
StartedAt: 2016-10-08 09:51:48 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 09:54:16 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 148.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Mulder2012.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/Mulder2012.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.12.0’
* 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 22.5Mb
  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.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.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 p.adjust pan_Arora2010
  pan_ext_Mulder2012 par parLapply pdf sd
Consider adding
  importFrom("grDevices", "graphics.off", "pdf")
  importFrom("graphics", "barplot", "par")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "na.omit",
             "p.adjust", "sd")
  importFrom("utils", "data", "getFromNamespace")
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 sizes of PDF files under ‘inst/doc’ ... 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-3.3-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.


Mulder2012.Rcheck/00install.out:

* 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)

Mulder2012.Rcheck/Mulder2012-Ex.timings:

nameusersystemelapsed
Arora2010.BMfitting0.0000.0000.001
Arora2010.InferPAN0.0000.0000.001
Arora2010.ModuleSearchByPvclust000
Arora2010.fig000
Arora2010.hypergeo0.0000.0000.001
Arora2010.module.visualize000
Arora2010.pipeline0.0000.0000.001
GSEARandomWalkFig0.0010.0000.000
Mulder2012.BMfitting0.0000.0000.001
Mulder2012.InferPAN0.0000.0000.001
Mulder2012.ModuleSearchByPvclust0.0010.0000.000
Mulder2012.PPIPre0.0000.0000.001
Mulder2012.PPIenrich000
Mulder2012.RNAiPre0.0010.0000.000
Mulder2012.fig0.0000.0000.001
Mulder2012.module.visualize0.0010.0000.000
Mulder2012.pipeline0.0000.0000.001
data-Arora20101.1600.0081.168
data-Mulder20120.7930.0000.792