BioC 3.1: CHECK report for KEGGgraph on petty
This page was generated on 2015-10-09 09:33:45 -0700 (Fri, 09 Oct 2015).
KEGGgraph 1.26.0 Jitao David Zhang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/KEGGgraph | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: KEGGgraph |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz |
StartedAt: 2015-10-08 23:54:52 -0700 (Thu, 08 Oct 2015) |
EndedAt: 2015-10-08 23:56:40 -0700 (Thu, 08 Oct 2015) |
EllapsedTime: 108.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: KEGGgraph.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGgraph’ can be installed ... [5s/6s] 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’ ‘XML’ ‘graph’
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
* 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’
getKEGGnodeData: no visible global function definition for ‘nodeData’
graphDensity: no visible global function definition for ‘numEdges’
graphDensity: no visible global function definition for ‘numNodes’
KEGGgraphLegend: no visible binding for global variable
‘KEGGEdgeSubtype’
KEGGpathway2Graph: no visible global function definition for
‘nodeDataDefaults<-’
KEGGpathway2Graph: no visible global function definition for
‘edgeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
‘ftM2graphNEL’
KEGGpathway2reactionGraph: no visible global function definition for
‘nodeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
‘edgeDataDefaults<-’
kgmlFileName2PathwayName: no visible binding for global variable
‘KEGGPATHID2NAME’
mergeKEGGgraphs : <anonymous>: no visible global function definition
for ‘nodeDataDefaults’
mergeKEGGgraphs : <anonymous>: no visible global function definition
for ‘edgeDataDefaults’
mergeKEGGgraphs: no visible global function definition for
‘nodeDataDefaults<-’
mergeKEGGgraphs: no visible global function definition for
‘edgeDataDefaults<-’
plotKEGGgraph: no visible global function definition for
‘edgeRenderInfo<-’
plotKEGGgraph: no visible global function definition for
‘nodeRenderInfo<-’
plotKEGGgraph: no visible global function definition for ‘layoutGraph’
plotKEGGgraph: no visible global function definition for ‘renderGraph’
randomSubGraph : <anonymous>: no visible global function definition for
‘subGraph’
setKEGGedgeData: no visible global function definition for
‘edgeDataDefaults<-’
setKEGGnodeData: no visible global function definition for
‘nodeDataDefaults<-’
subGraphByNodeType: no visible global function definition for
‘subGraph’
subKEGGgraph: no visible global function definition for ‘subGraph’
subKEGGgraph: no visible global function definition for
‘nodeDataDefaults’
subKEGGgraph: no visible global function definition for
‘edgeDataDefaults’
subKEGGgraph: no visible global function definition for
‘nodeDataDefaults<-’
subKEGGgraph: no visible global function definition for
‘edgeDataDefaults<-’
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 ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘kegg2graph.R’ [15s/15s]
Running ‘testGraph.R’ [2s/2s]
[17s/17s] 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/KEGGgraph.Rcheck/00check.log’
for details.
KEGGgraph.Rcheck/00install.out:
* 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
* DONE (KEGGgraph)
KEGGgraph.Rcheck/KEGGgraph-Ex.timings:
name | user | system | elapsed
|
KEGGEdge-class | 0.657 | 0.005 | 0.661 |
|
KEGGEdgeSubType-class | 0.001 | 0.000 | 0.001 |
|
KEGGEdgeSubtype | 0.013 | 0.002 | 0.014 |
|
KEGGGraphics-class | 0.002 | 0.000 | 0.002 |
|
KEGGGroup-class | 0.002 | 0.000 | 0.002 |
|
KEGGNode-class | 0.489 | 0.002 | 0.491 |
|
KEGGPathway-class | 1.038 | 0.015 | 1.055 |
|
KEGGPathwayInfo-class | 0.375 | 0.003 | 0.377 |
|
KEGGReaction-class | 0.679 | 0.003 | 0.682 |
|
KEGGpathway2Graph | 0.457 | 0.003 | 0.461 |
|
KEGGpathway2reactionGraph | 0.906 | 0.003 | 0.911 |
|
expandKEGGPathway | 1.124 | 0.003 | 1.128 |
|
getDisplayName-methods | 0.427 | 0.002 | 0.428 |
|
getEntryID-methods | 0.413 | 0.002 | 0.413 |
|
getKEGGID-methods | 0.317 | 0.001 | 0.319 |
|
getKEGGgeneLink-methods | 0.001 | 0.000 | 0.001 |
|
getKEGGnodeData | 1.427 | 0.006 | 1.434 |
|
getKGMLurl | 0.006 | 0.002 | 0.079 |
|
getName-methods | 0.585 | 0.002 | 0.588 |
|
getNamedElement | 0.001 | 0.000 | 0.001 |
|
getPathwayInfo-methods | 0.592 | 0.002 | 0.594 |
|
getReactions-methods | 0.874 | 0.003 | 0.877 |
|
getRgraphvizEdgeNames | 0.003 | 0.000 | 0.003 |
|
getSubtype-methods | 0.548 | 0.002 | 0.551 |
|
getTitle-methods | 0.593 | 0.002 | 0.597 |
|
getType-methods | 0.897 | 0.004 | 0.901 |
|
graphDensity | 0.003 | 0.000 | 0.003 |
|
isHomoList | 0.002 | 0.000 | 0.002 |
|
mergeKEGGgraphs | 2.550 | 0.011 | 2.568 |
|
neighborhood | 0.346 | 0.005 | 0.353 |
|
parseKGML | 0.489 | 0.002 | 0.491 |
|
parseKGML2DataFrame | 3.245 | 0.016 | 3.263 |
|
parseKGML2Graph | 1.406 | 0.007 | 1.414 |
|
plotKEGGgraph | 2.547 | 0.014 | 2.563 |
|
pvalue2asterisk | 0.002 | 0.000 | 0.002 |
|
queryKEGGsubgraph | 1.548 | 0.006 | 1.559 |
|
randomSubGraph | 0.026 | 0.001 | 0.026 |
|
splitKEGGgroup | 0.480 | 0.002 | 0.482 |
|
subGraphByNodeType | 1.300 | 0.005 | 1.307 |
|
subKEGGgraph | 1.401 | 0.005 | 1.407 |
|
translateKEGGID2GeneID | 0.002 | 0.000 | 0.002 |
|
translateKEGGgraph | 1.504 | 0.005 | 1.510 |
|