RCytoscape 1.21.1
Paul Shannon
| Snapshot Date: 2016-04-04 17:20:23 -0700 (Mon, 04 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCytoscape | | Last Changed Rev: 112953 / Revision: 115792 | | Last Changed Date: 2016-01-27 10:46:33 -0800 (Wed, 27 Jan 2016) |
| 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 | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### rm -rf RCytoscape.buildbin-libdir RCytoscape.Rcheck && mkdir RCytoscape.buildbin-libdir RCytoscape.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCytoscape.buildbin-libdir RCytoscape_1.21.1.tar.gz >RCytoscape.Rcheck\00install.out 2>&1 && cp RCytoscape.Rcheck\00install.out RCytoscape-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RCytoscape.buildbin-libdir --install="check:RCytoscape-install.out" --force-multiarch --no-vignettes --timings --no-examples RCytoscape_1.21.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RCytoscape.Rcheck'
* using R version 3.3.0 alpha (2016-03-28 r70390)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-examples --no-vignettes'
* checking for file 'RCytoscape/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCytoscape' version '1.21.1'
* 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 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
* 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'RCytoscape_unit_tests.R' [0s]
[1s] OK
** running tests for arch 'x64' ...
Running 'RCytoscape_unit_tests.R' [1s]
[1s] 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: 4 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/RCytoscape.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'RCytoscape' ...
** R
** 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 'RCytoscape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCytoscape' as RCytoscape_1.21.1.zip
* DONE (RCytoscape)