BioC 2.12: CHECK report for NCIgraph on moscato2

Package: NCIgraph

Version: 1.7.0

Command: rm -rf NCIgraph.buildbin-libdir && mkdir NCIgraph.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NCIgraph.buildbin-libdir NCIgraph_1.7.0.tar.gz >NCIgraph-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=NCIgraph.buildbin-libdir --install="check:NCIgraph-install.out" --force-multiarch --no-vignettes --timings NCIgraph_1.7.0.tar.gz && mv NCIgraph.buildbin-libdir/* NCIgraph.Rcheck/ && rmdir NCIgraph.buildbin-libdir

StartedAt: 2013-03-25 03:47:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:49:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 126.5 seconds

RetCode: 0

Status: OK

CheckDir: NCIgraph.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/NCIgraph.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NCIgraph/DESCRIPTION' ... OK
* this is package 'NCIgraph' version '1.7.0'
* 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 'NCIgraph' 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
getNCIPathways: warning in existing.CytoscapeWindow(w, copy.graph =
  TRUE): partial argument match of 'copy.graph' to
  'copy.graph.from.cytoscape.to.R'
* 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 examples ...
** running examples for arch 'i386' ... [28s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getNCIPathways      8.48      0    8.49
getSubtype.NCIgraph 8.28      0    8.29
translateNCI2GeneID 7.89      0    7.90
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
translateNCI2GeneID 9.56   0.00    9.57
getSubtype.NCIgraph 9.44   0.00    9.44
getNCIPathways      8.97   0.01    8.98
* 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 was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/NCIgraph.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'NCIgraph' ...
** R
** data
** 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
   'NCIgraph.Rnw' 
** 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 'NCIgraph' ...
** 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 'NCIgraph' as NCIgraph_1.7.0.zip
* DONE (NCIgraph)

Summary

Command output