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BioC 3.2: CHECK report for KEGGgraph on moscato1

This page was generated on 2016-04-23 10:16:50 -0700 (Sat, 23 Apr 2016).

Package 553/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGgraph 1.28.0
Jitao David Zhang
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/KEGGgraph
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  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: KEGGgraph
Version: 1.28.0
Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.28.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.28.0.tar.gz
StartedAt: 2016-04-23 04:00:10 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:03:21 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 190.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: KEGGgraph.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.28.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/KEGGgraph.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 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.28.0'
* 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 'KEGGgraph' can be installed ... OK
* checking installed package size ... OK
* 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
* 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' call to 'KEGG.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.subtypeDisplay: no visible binding for global variable
  'KEGGEdgeSubtype'
KEGGgraphLegend: no visible binding for global variable
  'KEGGEdgeSubtype'
kgmlFileName2PathwayName: no visible binding for global variable
  'KEGGPATHID2NAME'
plotKEGGgraph: no visible global function definition for 'layoutGraph'
plotKEGGgraph: no visible global function definition for 'renderGraph'
subtypeDisplay,graph : .local: no visible binding for global variable
  'test'
subtypeDisplay,graph : .local: no visible binding for global variable
  'keggeEdgesDisplay'
* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [30s] OK
** running examples for arch 'x64' ... [31s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'kegg2graph.R' [12s]
  Running 'testGraph.R' [2s]
 [15s] OK
** running tests for arch 'x64' ...
  Running 'kegg2graph.R' [16s]
  Running 'testGraph.R' [2s]
 [19s] 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/KEGGgraph.Rcheck/00check.log'
for details.


KEGGgraph.Rcheck/00install.out:


install for i386

* installing *source* package 'KEGGgraph' ...
** R
** data
** 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 'KEGGgraph' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGgraph' as KEGGgraph_1.28.0.zip
* DONE (KEGGgraph)

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

nameusersystemelapsed
KEGGEdge-class0.780.000.78
KEGGEdgeSubType-class000
KEGGEdgeSubtype0.040.000.03
KEGGGraphics-class000
KEGGGroup-class000
KEGGNode-class0.450.000.45
KEGGPathway-class0.810.000.81
KEGGPathwayInfo-class0.560.000.56
KEGGReaction-class0.920.000.92
KEGGpathway2Graph0.550.000.54
KEGGpathway2reactionGraph0.700.000.71
expandKEGGPathway0.810.010.82
getDisplayName-methods0.470.000.49
getEntryID-methods0.510.000.51
getKEGGID-methods0.280.000.28
getKEGGgeneLink-methods000
getKEGGnodeData1.30.01.3
getKGMLurl0.000.001.49
getName-methods0.470.000.47
getNamedElement000
getPathwayInfo-methods0.540.000.55
getReactions-methods0.830.000.82
getRgraphvizEdgeNames000
getSubtype-methods0.410.000.41
getTitle-methods0.560.000.56
getType-methods0.580.000.57
graphDensity000
isHomoList000
mergeKEGGgraphs1.820.001.83
neighborhood0.220.000.22
parseKGML0.350.000.34
parseKGML2DataFrame2.270.022.29
parseKGML2Graph1.410.001.41
plotKEGGgraph1.960.003.18
pvalue2asterisk000
queryKEGGsubgraph1.060.001.06
randomSubGraph0.040.000.03
splitKEGGgroup0.510.000.52
subGraphByNodeType1.620.001.62
subKEGGgraph1.390.001.39
translateKEGGID2GeneID000
translateKEGGgraph1.330.001.33

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

nameusersystemelapsed
KEGGEdge-class1.140.001.14
KEGGEdgeSubType-class000
KEGGEdgeSubtype0.010.000.01
KEGGGraphics-class000
KEGGGroup-class000
KEGGNode-class0.50.00.5
KEGGPathway-class1.080.001.07
KEGGPathwayInfo-class0.530.000.53
KEGGReaction-class0.900.000.91
KEGGpathway2Graph0.520.000.51
KEGGpathway2reactionGraph0.970.000.97
expandKEGGPathway0.930.000.94
getDisplayName-methods0.500.000.49
getEntryID-methods0.630.000.63
getKEGGID-methods0.330.000.33
getKEGGgeneLink-methods000
getKEGGnodeData1.20.01.2
getKGMLurl0.020.000.75
getName-methods0.440.000.43
getNamedElement000
getPathwayInfo-methods0.430.000.44
getReactions-methods0.660.000.66
getRgraphvizEdgeNames000
getSubtype-methods0.480.000.48
getTitle-methods0.380.000.37
getType-methods0.670.000.68
graphDensity000
isHomoList000
mergeKEGGgraphs2.570.002.57
neighborhood0.190.020.20
parseKGML0.40.00.4
parseKGML2DataFrame2.650.002.66
parseKGML2Graph1.490.001.48
plotKEGGgraph2.540.012.56
pvalue2asterisk0.010.000.01
queryKEGGsubgraph1.670.001.67
randomSubGraph0.010.000.01
splitKEGGgroup0.610.000.61
subGraphByNodeType1.160.001.15
subKEGGgraph1.250.001.25
translateKEGGID2GeneID000
translateKEGGgraph1.510.001.51