DEGraph 1.21.0
Laurent Jacob
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf DEGraph.buildbin-libdir DEGraph.Rcheck && mkdir DEGraph.buildbin-libdir DEGraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.21.0.tar.gz >DEGraph.Rcheck\00install.out 2>&1 && cp DEGraph.Rcheck\00install.out DEGraph-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.21.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DEGraph.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 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.21.0'
* 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 '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 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getKEGGPathways 6.76 0.00 10.56
plotValuedGraph 6.37 0.06 8.36
testOneGraph 5.39 0.01 5.39
** running examples for arch 'x64' ... [55s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getKEGGPathways 7.64 0.03 7.86
plotValuedGraph 7.51 0.03 7.61
testOneGraph 5.56 0.02 5.59
hyper.test 5.10 0.01 5.12
BS.test 5.08 0.00 5.10
AN.test 4.95 0.05 5.16
* 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
'D:/biocbld/bbs-3.2-bioc/meat/DEGraph.Rcheck/00check.log'
for details.
install for i386
* 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.
install for x64
* installing *source* package 'DEGraph' ...
** 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.
* MD5 sums
packaged installation of 'DEGraph' as DEGraph_1.21.0.zip
* DONE (DEGraph)