RCytoscape 1.22.0 Paul Shannon
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RCytoscape | Last Changed Rev: 117079 / Revision: 122332 | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ TIMEOUT ] | | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RCytoscape.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCytoscape/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCytoscape’ version ‘1.22.0’
* 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 ‘RCytoscape’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘XMLRPC’
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
Namespace in Imports field not imported from: ‘BiocGenerics’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGraphToGraph,CytoscapeWindowClass: warning in
.sendNodeAttributesForGraph(obj, other.graph, attr = attribute.name):
partial argument match of 'attr' to 'attribute.name'
addGraphToGraph,CytoscapeWindowClass: warning in
.sendEdgeAttributesForGraph(obj, other.graph, attr = attribute.name):
partial argument match of 'attr' to 'attribute.name'
.BBSOverride: no visible global function definition for ‘as’
.multiGraphToNodePairTable: no visible global function definition for
‘edgeSets’
is.classic.graph: no visible global function definition for ‘is’
is.multiGraph: no visible global function definition for ‘is’
makeRandomGraph: no visible global function definition for
‘randomGraph’
valid.graph: no visible global function definition for ‘slotNames’
valid.graph: no visible global function definition for ‘is’
valid.title: no visible global function definition for ‘slotNames’
valid.uri: no visible global function definition for ‘slotNames’
valid.window.id: no visible global function definition for ‘slotNames’
validCyWin: no visible global function definition for ‘is’
restoreLayout,CytoscapeWindowClass: no visible binding for global
variable ‘custom.layout’
restoreLayout,CytoscapeWindowClass : <anonymous>: no visible binding
for global variable ‘custom.layout’
setEdgeAttributesDirect,CytoscapeWindowClass: no visible binding for
'<<-' assignment to ‘timing.info’
setEdgeAttributesDirect,CytoscapeWindowClass: no visible binding for
global variable ‘timing.info’
Undefined global functions or variables:
as custom.layout edgeSets is randomGraph slotNames timing.info
Consider adding
importFrom("methods", "as", "is", "slotNames")
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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...