DEGraph 1.20.0
Laurent Jacob
| 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/DEGraph | | 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 | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DEGraph_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DEGraph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGraph/DESCRIPTION’ ... OK
* this is package ‘DEGraph’ version ‘1.20.0’
* 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 ‘DEGraph’ can be installed ... [4s/5s] 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 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
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
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
‘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 ‘enter’
getSignedGraph: no visible global function definition for ‘exit’
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’
plotValuedGraph: no visible binding for global variable ‘Arguments’
plotValuedGraph: no visible global function definition for ‘pushState’
plotValuedGraph: no visible global function definition for ‘popState’
randomWAMGraph: no visible binding for global variable ‘Arguments’
randomWAMGraph: no visible global function definition for ‘pushState’
randomWAMGraph: no visible global function definition for ‘popState’
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’
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 ‘exit’
writeAdjacencyMatrix2KGML: no visible binding for global variable
‘Arguments’
writeAdjacencyMatrix2KGML: no visible global function definition for
‘pushState’
writeAdjacencyMatrix2KGML: no visible global function definition for
‘popState’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/45s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getKEGGPathways 4.417 0.005 6.825
plotValuedGraph 3.325 0.019 7.036
testOneGraph 2.648 0.010 5.229
* 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
‘/home/biocbuild/bbs-3.1-bioc/meat/DEGraph.Rcheck/00check.log’
for details.
* installing *source* package ‘DEGraph’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (DEGraph)