BioC 2.12: CHECK report for RCytoscape on moscato2

Package: RCytoscape

Version: 1.10.0

Command: rm -rf RCytoscape.buildbin-libdir && mkdir RCytoscape.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCytoscape.buildbin-libdir RCytoscape_1.10.0.tar.gz >RCytoscape-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=RCytoscape.buildbin-libdir --install="check:RCytoscape-install.out" --force-multiarch --no-vignettes --timings --no-examples RCytoscape_1.10.0.tar.gz && mv RCytoscape.buildbin-libdir/* RCytoscape.Rcheck/ && rmdir RCytoscape.buildbin-libdir

StartedAt: 2013-10-09 03:48:32 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:50:32 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 120.1 seconds

RetCode: 0

Status: OK

CheckDir: RCytoscape.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/RCytoscape.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-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 '1.10.0'
* 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 whether package 'RCytoscape' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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'
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'
* 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 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' [0s]
 [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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/RCytoscape.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'RCytoscape' ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is 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
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class

install for x64

* installing *source* package 'RCytoscape' ...
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
* MD5 sums
packaged installation of 'RCytoscape' as RCytoscape_1.10.0.zip
* DONE (RCytoscape)

BioC 2.12: CHECK report for RCytoscape on moscato2

Summary

Command output