BioC 2.9: CHECK report for KEGGgraph on moscato1

Package: KEGGgraph

Version: 1.9.0

Command: mkdir KEGGgraph.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.9.0.tar.gz >KEGGgraph-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.9.0.tar.gz && mv KEGGgraph.buildbin-libdir/* KEGGgraph.Rcheck/ && rmdir KEGGgraph.buildbin-libdir

StartedAt: 2011-07-07 05:28:03 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:31:41 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 218.4 seconds

RetCode: 0

Status: OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-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 '1.9.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'KEGGgraph' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                             old_size new_size compress
  colorectalcancerSPIA.RData    955Kb    824Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* checking tests ...
** running tests for arch 'i386'
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 OK
** running tests for arch 'x64'
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK


install for i386

* installing *source* package 'KEGGgraph' ...
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'graph'

The following object(s) are masked from 'package:XML':

    addNode

Loading required package: grid
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'KEGGgraph.Rnw' 
   'KEGGgraphApp.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'KEGGgraph' ...
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
* MD5 sums
packaged installation of 'KEGGgraph' as KEGGgraph_1.9.0.zip

* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.98	0.01	1.00
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.62	0.00	0.63
KEGGPathway-class	1.11	0.00	1.10
KEGGPathwayInfo-class	0.61	0.00	0.61
KEGGReaction-class	0.92	0.00	0.92
KEGGpathway2Graph	0.68	0.00	0.69
KEGGpathway2reactionGraph	1.05	0.00	1.04
expandKEGGPathway	1.65	0.00	1.65
getDisplayName-methods	0.69	0.00	0.69
getEntryID-methods	0.61	0.00	0.61
getKEGGID-methods	0.29	0.00	0.30
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	2.39	0.00	2.39
getKGMLurl	0.00	0.00	22.88
getName-methods	0.54	0.02	0.57
getNamedElement	0	0	0
getPathwayInfo-methods	0.57	0.00	0.58
getReactions-methods	1	0	1
getRgraphvizEdgeNames	0.02	0.00	0.01
getSubtype-methods	0.61	0.00	0.61
getTitle-methods	0.65	0.00	0.66
getType-methods	0.95	0.00	0.95
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	2.98	0.00	2.98
neighborhood	0.03	0.00	0.04
parseKGML	0.61	0.00	0.60
parseKGML2Graph	1.57	0.00	1.58
plotKEGGgraph	3.34	0.00	3.34
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.62	0.00	1.62
randomSubGraph	0.02	0.00	0.01
splitKEGGgroup	0.59	0.00	0.59
subGraphByNodeType	1.67	0.01	1.70
subKEGGgraph	1.56	0.00	1.56
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.62	0.00	1.69

Summary

Command output