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Package 255/479HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.9.0
Jitao David Zhang
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGgraph
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ ERROR ] OK 

Summary

Package: KEGGgraph
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.9.0.tar.gz
StartedAt: 2011-07-07 03:59:42 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:01:55 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 133.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: KEGGgraph.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* checking tests ...
  Running 'kegg2graph.R'
/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 60274 Segmentation fault      ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
 ERROR
Running the tests in 'tests/kegg2graph.R' failed.
Last 13 lines of output:
  address 0xc000001b, cause 'memory not mapped'
  
  Traceback:
   1: as.list(X)
   2: lapply(X = X, FUN = FUN, ...)
   3: sapply(agn, function(n) {    c(getNodeRW(n) + getNodeLW(n), getNodeHeight(n))})
   4: .local(x, y, ...)
   5: plot(g, y, ...)
   6: plot(g, y, ...)
   7: .local(x, y, ...)
   8: plot(gR.compact, "twopi")
   9: plot(gR.compact, "twopi")
  aborting ...

KEGGgraph.Rcheck/00install.out:

* 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

* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class1.5750.0191.622
KEGGEdgeSubType-class0.0010.0000.001
KEGGEdgeSubtype0.0110.0010.013
KEGGGraphics-class0.0010.0000.001
KEGGGroup-class0.0010.0010.001
KEGGNode-class0.8870.0080.924
KEGGPathway-class1.4790.0121.511
KEGGPathwayInfo-class0.8640.0070.878
KEGGReaction-class1.4640.0101.546
KEGGpathway2Graph1.0740.0091.095
KEGGpathway2reactionGraph1.5030.0111.551
expandKEGGPathway2.0530.0082.090
getDisplayName-methods0.9350.0070.977
getEntryID-methods0.9010.0050.915
getKEGGID-methods0.4520.0030.459
getKEGGgeneLink-methods0.0010.0000.000
getKEGGnodeData2.4460.0122.483
getKGMLurl0.0080.0180.028
getName-methods0.9450.0280.986
getNamedElement000
getPathwayInfo-methods0.8480.0050.865
getReactions-methods1.4940.0071.515
getRgraphvizEdgeNames0.0040.0000.004
getSubtype-methods0.9240.0070.945
getTitle-methods0.8450.0050.859
getType-methods1.4420.0091.472
graphDensity0.0050.0000.005
isHomoList0.0010.0000.001
mergeKEGGgraphs4.4940.0254.566
neighborhood0.0370.0010.039
parseKGML0.9130.0050.929
parseKGML2Graph2.6600.0112.691
plotKEGGgraph4.7580.0314.900
pvalue2asterisk0.0000.0000.001
queryKEGGsubgraph2.4670.0112.517
randomSubGraph0.0540.0010.055
splitKEGGgroup0.9610.0070.979
subGraphByNodeType2.3670.0072.396
subKEGGgraph2.4310.0082.471
translateKEGGID2GeneID0.0000.0000.001
translateKEGGgraph2.6030.0132.646