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CHECK report for GOFunction on tokay2

This page was generated on 2018-10-17 08:35:30 -0400 (Wed, 17 Oct 2018).

Package 628/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOFunction 1.28.0
Jing Wang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GOFunction
Branch: RELEASE_3_7
Last Commit: 0f97c4d
Last Changed Date: 2018-04-30 10:35:19 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOFunction
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOFunction.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GOFunction_1.28.0.tar.gz
StartedAt: 2018-10-17 02:28:28 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:50:08 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1299.4 seconds
RetCode: 0
Status:  OK  
CheckDir: GOFunction.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOFunction.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GOFunction_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GOFunction.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOFunction/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GOFunction' version '1.28.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GOFunction 518.03  81.54  599.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GOFunction 504.75  80.19  586.47
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/GOFunction.Rcheck/00check.log'
for details.



Installation output

GOFunction.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GOFunction_1.28.0.tar.gz && rm -rf GOFunction.buildbin-libdir && mkdir GOFunction.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOFunction.buildbin-libdir GOFunction_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GOFunction_1.28.0.zip && rm GOFunction_1.28.0.tar.gz GOFunction_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  582k  100  582k    0     0  9646k      0 --:--:-- --:--:-- --:--:-- 10.5M

install for i386

* installing *source* package 'GOFunction' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GOFunction'
    finding HTML links ... done
    GOFunction-package                      html  
    GOFunction                              html  
    createGODAG                             html  
    enrichmentFunction                      html  
    globalRedundancy                        html  
    interestGenes                           html  
    localRedundancy                         html  
    refGenes                                html  
    showSigNodes                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GOFunction' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOFunction' as GOFunction_1.28.0.zip
* DONE (GOFunction)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GOFunction' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

GOFunction.Rcheck/examples_i386/GOFunction-Ex.timings

nameusersystemelapsed
GOFunction518.03 81.54599.96

GOFunction.Rcheck/examples_x64/GOFunction-Ex.timings

nameusersystemelapsed
GOFunction504.75 80.19586.47