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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:DEGraph.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings DEGraph_1.59.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DEGraph.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DEGraph/DESCRIPTION’ ... OK
* this is package ‘DEGraph’ version ‘1.59.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEGraph’ 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:
  ‘graph’ ‘KEGGgraph’ ‘lattice’ ‘RBGL’ ‘rrcov’ ‘Rgraphviz’ ‘NCIgraph’
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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘R.utils’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘graph:::getIndices’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AN.test: no visible global function definition for ‘var’
BS.test: no visible global function definition for ‘pnorm’
getConnectedComponentList: no visible binding for global variable
  ‘Arguments’
getConnectedComponentList: no visible global function definition for
  ‘pushState’
getConnectedComponentList: no visible global function definition for
  ‘popState’
getKEGGPathways: no visible binding for global variable ‘Arguments’
getKEGGPathways: no visible global function definition for ‘pushState’
getKEGGPathways: no visible global function definition for ‘popState’
getKEGGPathways: no visible global function definition for ‘str’
getKEGGPathways: no visible global function definition for
  ‘ProgressBar’
getKEGGPathways: no visible global function definition for ‘reset’
getKEGGPathways : <anonymous>: no visible global function definition
  for ‘increase’
getSignedGraph: no visible binding for global variable ‘Arguments’
getSignedGraph: no visible global function definition for ‘pushState’
getSignedGraph: no visible global function definition for ‘popState’
getSignedGraph: no visible global function definition for ‘str’
getSignedGraph: no visible global function definition for ‘enter’
getSignedGraph: no visible global function definition for ‘exit’
getSignedGraph: no visible global function definition for ‘as’
graph.T2.test: no visible global function definition for ‘as’
hyper.test: no visible binding for global variable ‘Arguments’
hyper.test: no visible global function definition for ‘pushState’
hyper.test: no visible global function definition for ‘popState’
hyper.test: no visible global function definition for ‘str’
hyper.test: no visible global function definition for ‘phyper’
plotValuedGraph: no visible global function definition for
  ‘heat.colors’
plotValuedGraph: no visible binding for global variable ‘Arguments’
plotValuedGraph: no visible global function definition for ‘pushState’
plotValuedGraph: no visible global function definition for ‘popState’
plotValuedGraph: no visible global function definition for ‘str’
plotValuedGraph: no visible global function definition for ‘quantile’
randomWAMGraph: no visible binding for global variable ‘Arguments’
randomWAMGraph: no visible global function definition for ‘pushState’
randomWAMGraph: no visible global function definition for ‘popState’
randomWAMGraph: no visible global function definition for ‘as’
testOneConnectedComponent: no visible binding for global variable
  ‘Arguments’
testOneConnectedComponent: no visible global function definition for
  ‘pushState’
testOneConnectedComponent: no visible global function definition for
  ‘popState’
testOneConnectedComponent: no visible global function definition for
  ‘enter’
testOneConnectedComponent: no visible global function definition for
  ‘exit’
testOneConnectedComponent: no visible global function definition for
  ‘as’
testOneConnectedComponent: no visible global function definition for
  ‘str’
testOneGraph: no visible binding for global variable ‘Arguments’
testOneGraph: no visible global function definition for ‘pushState’
testOneGraph: no visible global function definition for ‘popState’
testOneGraph: no visible global function definition for ‘enter’
testOneGraph: no visible global function definition for
  ‘translateNCI2GeneID’
testOneGraph: no visible global function definition for ‘str’
testOneGraph: no visible global function definition for ‘exit’
twoSampleFromGraph: no visible global function definition for ‘rnorm’
writeAdjacencyMatrix2KGML: no visible binding for global variable
  ‘Arguments’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘pushState’
writeAdjacencyMatrix2KGML: no visible global function definition for
  ‘popState’
writeAdjacencyMatrix2KGML : <anonymous>: no visible global function
  definition for ‘na.omit’
Undefined global functions or variables:
  Arguments ProgressBar as enter exit heat.colors increase na.omit
  phyper pnorm popState pushState quantile reset rnorm str
  translateNCI2GeneID var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("methods", "as")
  importFrom("stats", "na.omit", "phyper", "pnorm", "quantile", "rnorm",
             "var")
  importFrom("utils", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getConnectedComponentList.Rd: graph-class, connectedComp
  getKEGGPathways.Rd: graph-class, parseKGML, KEGGpathway2Graph
  getSignedGraph.Rd: graph-class
  graph.T2.test.Rd: graphAM-class, graphNEL-class, T2.test
  plotValuedGraph.Rd: graph-class, plotKEGGgraph
  randomWAMGraph.Rd: graphAM-class
  testOneConnectedComponent.Rd: graph-class
  testOneGraph.Rd: graph-class
  writeAdjacencyMatrix2KGML.Rd: parseKGML2Graph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/DEGraph.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL DEGraph
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘DEGraph’ ...
** this is package ‘DEGraph’ version ‘1.59.0’
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEGraph)