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CHECK report for GOFunction on merida1

This page was generated on 2019-04-16 11:55:37 -0400 (Tue, 16 Apr 2019).

Package 661/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOFunction 1.30.0
Jing Wang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GOFunction
Branch: RELEASE_3_8
Last Commit: 9891bd6
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GOFunction
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOFunction.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOFunction_1.30.0.tar.gz
StartedAt: 2019-04-16 00:20:28 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:29:07 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 518.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GOFunction.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOFunction.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOFunction_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GOFunction.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.30.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOFunction 402.991 20.658 430.816
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GOFunction.Rcheck/00check.log’
for details.



Installation output

GOFunction.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GOFunction
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GOFunction’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOFunction)

Tests output


Example timings

GOFunction.Rcheck/GOFunction-Ex.timings

nameusersystemelapsed
GOFunction402.991 20.658430.816