BioC 3.1: CHECK report for KEGGgraph on morelia
This page was generated on 2015-10-09 09:38:58 -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: 2015-10-09 03:18:26 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 03:19:36 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 70.2 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 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [3s/3s] 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’
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<-’
getKEGGnodeData: no visible global function definition for ‘nodeData’
graphDensity: no visible global function definition for ‘numEdges’
graphDensity: no visible global function definition for ‘numNodes’
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 ... [21s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘kegg2graph.R’ [9s/9s]
Running ‘testGraph.R’ [1s/1s]
[11s/11s] 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 | 0.556 | 0.013 | 0.569 |
|
KEGGEdgeSubType-class | 0.001 | 0.000 | 0.002 |
|
KEGGEdgeSubtype | 0.011 | 0.001 | 0.012 |
|
KEGGGraphics-class | 0.001 | 0.001 | 0.001 |
|
KEGGGroup-class | 0.001 | 0.000 | 0.002 |
|
KEGGNode-class | 0.227 | 0.001 | 0.228 |
|
KEGGPathway-class | 0.462 | 0.034 | 0.496 |
|
KEGGPathwayInfo-class | 0.357 | 0.020 | 0.377 |
|
KEGGReaction-class | 0.513 | 0.036 | 0.549 |
|
KEGGpathway2Graph | 0.380 | 0.003 | 0.383 |
|
KEGGpathway2reactionGraph | 0.696 | 0.005 | 0.704 |
|
expandKEGGPathway | 0.699 | 0.013 | 0.714 |
|
getDisplayName-methods | 0.399 | 0.017 | 0.416 |
|
getEntryID-methods | 0.344 | 0.057 | 0.401 |
|
getKEGGID-methods | 0.235 | 0.004 | 0.238 |
|
getKEGGgeneLink-methods | 0.000 | 0.000 | 0.001 |
|
getKEGGnodeData | 0.843 | 0.048 | 0.892 |
|
getKGMLurl | 0.004 | 0.002 | 0.008 |
|
getName-methods | 0.359 | 0.022 | 0.381 |
|
getNamedElement | 0.001 | 0.000 | 0.001 |
|
getPathwayInfo-methods | 0.372 | 0.001 | 0.373 |
|
getReactions-methods | 0.638 | 0.012 | 0.650 |
|
getRgraphvizEdgeNames | 0.003 | 0.000 | 0.003 |
|
getSubtype-methods | 0.331 | 0.008 | 0.338 |
|
getTitle-methods | 0.351 | 0.027 | 0.377 |
|
getType-methods | 0.646 | 0.002 | 0.649 |
|
graphDensity | 0.001 | 0.000 | 0.002 |
|
isHomoList | 0.002 | 0.000 | 0.001 |
|
mergeKEGGgraphs | 1.669 | 0.039 | 1.713 |
|
neighborhood | 0.147 | 0.004 | 0.174 |
|
parseKGML | 0.337 | 0.053 | 0.390 |
|
parseKGML2DataFrame | 2.276 | 0.222 | 2.501 |
|
parseKGML2Graph | 0.878 | 0.029 | 0.907 |
|
plotKEGGgraph | 1.521 | 0.012 | 1.534 |
|
pvalue2asterisk | 0.001 | 0.000 | 0.001 |
|
queryKEGGsubgraph | 0.795 | 0.095 | 0.891 |
|
randomSubGraph | 0.014 | 0.004 | 0.018 |
|
splitKEGGgroup | 0.356 | 0.017 | 0.374 |
|
subGraphByNodeType | 0.847 | 0.020 | 0.867 |
|
subKEGGgraph | 0.980 | 0.108 | 1.088 |
|
translateKEGGID2GeneID | 0.001 | 0.000 | 0.000 |
|
translateKEGGgraph | 0.870 | 0.047 | 0.918 |
|