BioC 2.12: CHECK report for DEGraph on moscato2

Package: DEGraph

Version: 1.12.0

Command: rm -rf DEGraph.buildbin-libdir && mkdir DEGraph.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.12.0.tar.gz >DEGraph-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.12.0.tar.gz && mv DEGraph.buildbin-libdir/* DEGraph.Rcheck/ && rmdir DEGraph.buildbin-libdir

StartedAt: 2013-10-09 01:49:04 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:53:52 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 287.6 seconds

RetCode: 0

Status: OK

CheckDir: DEGraph.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/DEGraph.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.12.0'
* 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 'DEGraph' 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 ... OK
* 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' ... [83s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getKEGGPathways 23.88   0.04   25.51
plotValuedGraph 10.92   0.08   11.00
testOneGraph     9.16   0.04    9.21
BS.test          5.85   0.07    5.91
AN.test          5.82   0.01    5.83
hyper.test       5.55   0.03    5.59
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getKEGGPathways 24.31   0.05   24.35
plotValuedGraph 12.74   0.06   12.81
testOneGraph     7.21   0.05    7.26
AN.test          6.56   0.04    6.64
BS.test          6.37   0.03    6.44
* 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


install for i386

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** 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 'DEGraph' ...
** 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 'DEGraph' as DEGraph_1.12.0.zip
* DONE (DEGraph)

BioC 2.12: CHECK report for DEGraph on moscato2

Summary

Command output