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BioC 3.5: CHECK report for GOFunction on malbec2

This page was generated on 2017-08-16 13:14:01 -0400 (Wed, 16 Aug 2017).

Package 572/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOFunction 1.24.0
Jing Wang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GOFunction
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOFunction
Version: 1.24.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOFunction_1.24.0.tar.gz
StartedAt: 2017-08-15 23:31:26 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:38:26 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 420.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GOFunction.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOFunction_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GOFunction.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 ‘GOFunction/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GOFunction’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘graph’ ‘Rgraphviz’ ‘GO.db’ ‘AnnotationDbi’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GOFunction’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘Biobase’ ‘graph’ ‘Rgraphviz’ ‘GO.db’ ‘AnnotationDbi’ ‘SparseM’
A package should be listed in only one of these fields.
* 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 to packages already attached by Depends:
  ‘GO.db’ ‘Rgraphviz’ ‘SparseM’ ‘graph’ ‘methods’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘GO.db’ ‘Rgraphviz’ ‘graph’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GO.db’ ‘Rgraphviz’ ‘graph’
  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
File ‘GOFunction/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

GOFunction: no visible global function definition for ‘nodes’
GOFunction: no visible global function definition for ‘write.csv’
createGODAG: no visible global function definition for ‘sparseM2Graph’
createGODAG: no visible global function definition for ‘graph2SparseM’
enrichmentFunction: no visible global function definition for ‘phyper’
enrichmentFunction: no visible global function definition for
  ‘p.adjust’
globalRedundancy : calculateEachTerm : calculateExtraTerm: no visible
  global function definition for ‘phyper’
localRedundancy: no visible global function definition for ‘phyper’
showSigNodes: no visible global function definition for
  ‘getDefaultAttrs’
showSigNodes: no visible global function definition for ‘heat.colors’
showSigNodes: no visible global function definition for ‘edgeWeights’
showSigNodes: no visible global function definition for ‘nodes’
showSigNodes: no visible global function definition for ‘bmp’
showSigNodes: no visible global function definition for ‘plot’
showSigNodes: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  bmp dev.off edgeWeights getDefaultAttrs graph2SparseM heat.colors
  nodes p.adjust phyper plot sparseM2Graph write.csv
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "heat.colors")
  importFrom("graphics", "plot")
  importFrom("stats", "p.adjust", "phyper")
  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
Examples with CPU or elapsed time > 5s
              user system elapsed
GOFunction 334.624 12.416 349.775
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GOFunction.Rcheck/00check.log’
for details.


GOFunction.Rcheck/00install.out:

* installing *source* package ‘GOFunction’ ...
** 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 (GOFunction)

GOFunction.Rcheck/GOFunction-Ex.timings:

nameusersystemelapsed
GOFunction334.624 12.416349.775