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BioC 3.1: CHECK report for RCytoscape on moscato2

This page was generated on 2015-10-09 09:28:55 -0700 (Fri, 09 Oct 2015).

Package 796/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCytoscape 1.18.0
Paul Shannon
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/RCytoscape
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 UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCytoscape
Version: 1.18.0
Command: rm -rf RCytoscape.buildbin-libdir RCytoscape.Rcheck && mkdir RCytoscape.buildbin-libdir RCytoscape.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCytoscape.buildbin-libdir RCytoscape_1.18.0.tar.gz >RCytoscape.Rcheck\00install.out 2>&1 && cp RCytoscape.Rcheck\00install.out RCytoscape-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RCytoscape.buildbin-libdir --install="check:RCytoscape-install.out" --force-multiarch --no-vignettes --timings --no-examples RCytoscape_1.18.0.tar.gz
StartedAt: 2015-10-09 05:23:26 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:24:56 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 90.6 seconds
RetCode: 0
Status:  OK  
CheckDir: RCytoscape.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RCytoscape.buildbin-libdir RCytoscape.Rcheck && mkdir RCytoscape.buildbin-libdir RCytoscape.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCytoscape.buildbin-libdir RCytoscape_1.18.0.tar.gz >RCytoscape.Rcheck\00install.out 2>&1 && cp RCytoscape.Rcheck\00install.out RCytoscape-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RCytoscape.buildbin-libdir --install="check:RCytoscape-install.out" --force-multiarch --no-vignettes --timings --no-examples RCytoscape_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RCytoscape.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.18.0'
* 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 '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'
.multiGraphToNodePairTable: no visible global function definition for
  'edgeSets'
makeRandomGraph: no visible global function definition for
  'randomGraph'
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 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' [0s]
 [0s] 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-3.1-bioc/meat/RCytoscape.Rcheck/00check.log'
for details.


RCytoscape.Rcheck/00install.out:


install for i386

* installing *source* package 'RCytoscape' ...
** R
** 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 'RCytoscape' ...
** 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 'RCytoscape' as RCytoscape_1.18.0.zip
* DONE (RCytoscape)