BioC 3.1: CHECK report for KEGGgraph on moscato2
This page was generated on 2015-10-09 09:28:26 -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
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Version: 1.26.0
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Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.26.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.26.0.tar.gz
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StartedAt: 2015-10-09 03:11:17 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 03:13:28 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 130.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: KEGGgraph.Rcheck
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Warnings: 0
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Command output
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### Running command:
###
### rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.26.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.26.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.26.0'
* 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 whether package 'KEGGgraph' can be installed ... 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
* 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'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [23s] OK
** running examples for arch 'x64' ... [26s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'kegg2graph.R' [9s]
Running 'testGraph.R' [2s]
[11s] OK
** running tests for arch 'x64' ...
Running 'kegg2graph.R' [11s]
Running 'testGraph.R' [1s]
[13s] 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
'E:/biocbld/bbs-3.1-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_1.26.0.zip
* DONE (KEGGgraph)
KEGGgraph.Rcheck/examples_i386/KEGGgraph-Ex.timings:
name | user | system | elapsed
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KEGGEdge-class | 0.60 | 0.00 | 0.59 |
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KEGGEdgeSubType-class | 0 | 0 | 0 |
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KEGGEdgeSubtype | 0.01 | 0.00 | 0.02 |
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KEGGGraphics-class | 0 | 0 | 0 |
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KEGGGroup-class | 0 | 0 | 0 |
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KEGGNode-class | 0.5 | 0.0 | 0.5 |
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KEGGPathway-class | 0.64 | 0.00 | 0.64 |
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KEGGPathwayInfo-class | 0.42 | 0.00 | 0.42 |
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KEGGReaction-class | 0.52 | 0.00 | 0.51 |
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KEGGpathway2Graph | 0.32 | 0.00 | 0.33 |
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KEGGpathway2reactionGraph | 0.53 | 0.00 | 0.53 |
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expandKEGGPathway | 0.63 | 0.00 | 0.63 |
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getDisplayName-methods | 0.31 | 0.00 | 0.31 |
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getEntryID-methods | 0.38 | 0.00 | 0.37 |
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getKEGGID-methods | 0.15 | 0.00 | 0.16 |
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getKEGGgeneLink-methods | 0 | 0 | 0 |
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getKEGGnodeData | 0.81 | 0.00 | 0.81 |
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getKGMLurl | 0.00 | 0.00 | 1.45 |
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getName-methods | 0.37 | 0.00 | 0.37 |
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getNamedElement | 0 | 0 | 0 |
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getPathwayInfo-methods | 0.33 | 0.01 | 0.34 |
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getReactions-methods | 0.53 | 0.00 | 0.53 |
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getRgraphvizEdgeNames | 0 | 0 | 0 |
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getSubtype-methods | 0.36 | 0.00 | 0.36 |
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getTitle-methods | 0.34 | 0.00 | 0.35 |
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getType-methods | 0.55 | 0.00 | 0.54 |
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graphDensity | 0.00 | 0.02 | 0.02 |
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isHomoList | 0 | 0 | 0 |
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mergeKEGGgraphs | 1.54 | 0.00 | 1.54 |
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neighborhood | 0.19 | 0.00 | 0.19 |
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parseKGML | 0.31 | 0.00 | 0.31 |
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parseKGML2DataFrame | 2.05 | 0.00 | 2.04 |
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parseKGML2Graph | 0.95 | 0.00 | 0.96 |
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plotKEGGgraph | 1.73 | 0.01 | 1.75 |
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pvalue2asterisk | 0 | 0 | 0 |
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queryKEGGsubgraph | 0.79 | 0.00 | 0.80 |
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randomSubGraph | 0.02 | 0.00 | 0.01 |
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splitKEGGgroup | 0.28 | 0.00 | 0.28 |
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subGraphByNodeType | 0.81 | 0.00 | 0.81 |
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subKEGGgraph | 0.79 | 0.00 | 0.79 |
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translateKEGGID2GeneID | 0 | 0 | 0 |
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translateKEGGgraph | 1.08 | 0.00 | 1.08 |
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KEGGgraph.Rcheck/examples_x64/KEGGgraph-Ex.timings:
name | user | system | elapsed
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KEGGEdge-class | 0.66 | 0.00 | 0.66 |
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KEGGEdgeSubType-class | 0 | 0 | 0 |
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KEGGEdgeSubtype | 0.01 | 0.00 | 0.01 |
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KEGGGraphics-class | 0 | 0 | 0 |
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KEGGGroup-class | 0 | 0 | 0 |
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KEGGNode-class | 0.34 | 0.00 | 0.35 |
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KEGGPathway-class | 0.61 | 0.00 | 0.60 |
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KEGGPathwayInfo-class | 0.33 | 0.00 | 0.33 |
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KEGGReaction-class | 0.61 | 0.00 | 0.61 |
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KEGGpathway2Graph | 0.39 | 0.00 | 0.39 |
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KEGGpathway2reactionGraph | 0.61 | 0.00 | 0.61 |
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expandKEGGPathway | 0.93 | 0.00 | 0.93 |
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getDisplayName-methods | 0.60 | 0.01 | 0.61 |
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getEntryID-methods | 0.63 | 0.00 | 0.62 |
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getKEGGID-methods | 0.29 | 0.00 | 0.30 |
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getKEGGgeneLink-methods | 0 | 0 | 0 |
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getKEGGnodeData | 1 | 0 | 1 |
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getKGMLurl | 0.00 | 0.00 | 0.98 |
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getName-methods | 0.36 | 0.00 | 0.36 |
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getNamedElement | 0 | 0 | 0 |
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getPathwayInfo-methods | 0.36 | 0.00 | 0.36 |
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getReactions-methods | 0.59 | 0.00 | 0.59 |
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getRgraphvizEdgeNames | 0 | 0 | 0 |
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getSubtype-methods | 0.36 | 0.00 | 0.36 |
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getTitle-methods | 0.37 | 0.00 | 0.37 |
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getType-methods | 0.67 | 0.00 | 0.67 |
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graphDensity | 0.02 | 0.00 | 0.01 |
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isHomoList | 0 | 0 | 0 |
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mergeKEGGgraphs | 1.92 | 0.00 | 1.92 |
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neighborhood | 0.17 | 0.00 | 0.17 |
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parseKGML | 0.39 | 0.00 | 0.39 |
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parseKGML2DataFrame | 2.89 | 0.00 | 2.89 |
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parseKGML2Graph | 1.06 | 0.02 | 1.08 |
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plotKEGGgraph | 1.7 | 0.0 | 1.7 |
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pvalue2asterisk | 0 | 0 | 0 |
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queryKEGGsubgraph | 0.98 | 0.00 | 0.98 |
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randomSubGraph | 0.02 | 0.00 | 0.01 |
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splitKEGGgroup | 0.37 | 0.00 | 0.38 |
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subGraphByNodeType | 0.97 | 0.01 | 0.98 |
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subKEGGgraph | 0.97 | 0.00 | 0.97 |
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translateKEGGID2GeneID | 0 | 0 | 0 |
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translateKEGGgraph | 1.02 | 0.00 | 1.09 |
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