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BioC 3.2: CHECK report for DEGraph on moscato1

This page was generated on 2016-04-23 10:17:34 -0700 (Sat, 23 Apr 2016).

Package 260/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGraph 1.22.0
Laurent Jacob
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DEGraph
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEGraph
Version: 1.22.0
Command: rm -rf DEGraph.buildbin-libdir DEGraph.Rcheck && mkdir DEGraph.buildbin-libdir DEGraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.22.0.tar.gz >DEGraph.Rcheck\00install.out 2>&1 && cp DEGraph.Rcheck\00install.out DEGraph-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.22.0.tar.gz
StartedAt: 2016-04-23 01:31:01 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:35:00 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 238.9 seconds
RetCode: 0
Status:  OK  
CheckDir: DEGraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEGraph.buildbin-libdir DEGraph.Rcheck && mkdir DEGraph.buildbin-libdir DEGraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.22.0.tar.gz >DEGraph.Rcheck\00install.out 2>&1 && cp DEGraph.Rcheck\00install.out DEGraph-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DEGraph.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.22.0'
* 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 whether package 'DEGraph' 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:
  'graph' 'KEGGgraph' 'lattice' 'RBGL' 'rrcov' 'Rgraphviz' 'NCIgraph'
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
Package in Depends field not imported from: 'R.utils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'graph:::getIndices'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getConnectedComponentList: no visible binding for global variable
  'Arguments'
getConnectedComponentList: no visible global function definition for
  'pushState'
getConnectedComponentList: no visible global function definition for
  'popState'
getKEGGPathways: no visible binding for global variable 'Arguments'
getKEGGPathways: no visible global function definition for 'pushState'
getKEGGPathways: no visible global function definition for 'popState'
getKEGGPathways: no visible global function definition for
  'ProgressBar'
getKEGGPathways: no visible global function definition for 'reset'
getKEGGPathways : <anonymous>: no visible global function definition
  for 'increase'
getSignedGraph: no visible binding for global variable 'Arguments'
getSignedGraph: no visible global function definition for 'pushState'
getSignedGraph: no visible global function definition for 'popState'
getSignedGraph: no visible global function definition for 'enter'
getSignedGraph: no visible global function definition for 'exit'
hyper.test: no visible binding for global variable 'Arguments'
hyper.test: no visible global function definition for 'pushState'
hyper.test: no visible global function definition for 'popState'
plotValuedGraph: no visible binding for global variable 'Arguments'
plotValuedGraph: no visible global function definition for 'pushState'
plotValuedGraph: no visible global function definition for 'popState'
randomWAMGraph: no visible binding for global variable 'Arguments'
randomWAMGraph: no visible global function definition for 'pushState'
randomWAMGraph: no visible global function definition for 'popState'
testOneConnectedComponent: no visible binding for global variable
  'Arguments'
testOneConnectedComponent: no visible global function definition for
  'pushState'
testOneConnectedComponent: no visible global function definition for
  'popState'
testOneConnectedComponent: no visible global function definition for
  'enter'
testOneConnectedComponent: no visible global function definition for
  'exit'
testOneGraph: no visible binding for global variable 'Arguments'
testOneGraph: no visible global function definition for 'pushState'
testOneGraph: no visible global function definition for 'popState'
testOneGraph: no visible global function definition for 'enter'
testOneGraph: no visible global function definition for
  'translateNCI2GeneID'
testOneGraph: no visible global function definition for 'exit'
writeAdjacencyMatrix2KGML: no visible binding for global variable
  'Arguments'
writeAdjacencyMatrix2KGML: no visible global function definition for
  'pushState'
writeAdjacencyMatrix2KGML: no visible global function definition for
  'popState'
* 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 ...
** running examples for arch 'i386' ... [56s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getKEGGPathways 6.90   0.02   11.19
testOneGraph    5.51   0.03    5.96
AN.test         5.05   0.00    5.07
plotValuedGraph 5.03   0.00    9.57
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getKEGGPathways 10.27   0.00   11.02
plotValuedGraph  7.11   0.01   10.26
BS.test          5.12   0.05    5.19
testOneGraph     4.97   0.02    5.10
AN.test          4.91   0.01    5.60
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/DEGraph.Rcheck/00check.log'
for details.


DEGraph.Rcheck/00install.out:


install for i386

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DEGraph' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGraph' as DEGraph_1.22.0.zip
* DONE (DEGraph)

DEGraph.Rcheck/examples_i386/DEGraph-Ex.timings:

nameusersystemelapsed
AN.test5.050.005.07
BS.test3.290.003.29
annLoi20080.270.000.26
classLoi20080.250.000.25
exprLoi20080.250.000.25
getConnectedComponentList2.260.012.28
getKEGGPathways 6.90 0.0211.19
getSignedGraph2.450.002.45
grListKEGG1.190.001.19
graph.T2.test1.550.021.56
hyper.test3.930.013.95
laplacianFromA0.210.010.49
plotValuedGraph5.030.009.57
randomWAMGraph0.270.000.48
testOneConnectedComponent2.160.002.17
testOneGraph5.510.035.96
twoSampleFromGraph0.290.000.51
writeAdjacencyMatrix2KGML0.250.020.48

DEGraph.Rcheck/examples_x64/DEGraph-Ex.timings:

nameusersystemelapsed
AN.test4.910.015.60
BS.test5.120.055.19
annLoi20080.210.000.22
classLoi20080.330.000.33
exprLoi20080.420.020.43
getConnectedComponentList3.820.003.83
getKEGGPathways10.27 0.0011.02
getSignedGraph2.870.002.87
grListKEGG1.230.011.25
graph.T2.test2.130.002.12
hyper.test4.930.034.96
laplacianFromA0.360.023.04
plotValuedGraph 7.11 0.0110.26
randomWAMGraph0.260.020.50
testOneConnectedComponent2.230.002.23
testOneGraph4.970.025.10
twoSampleFromGraph0.310.010.54
writeAdjacencyMatrix2KGML0.310.000.53