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BioC 3.1: CHECK report for NCIgraph on moscato2

This page was generated on 2015-10-09 09:29:12 -0700 (Fri, 09 Oct 2015).

Package 649/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NCIgraph 1.16.0
Laurent Jacob
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/NCIgraph
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: NCIgraph
Version: 1.16.0
Command: rm -rf NCIgraph.buildbin-libdir NCIgraph.Rcheck && mkdir NCIgraph.buildbin-libdir NCIgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NCIgraph.buildbin-libdir NCIgraph_1.16.0.tar.gz >NCIgraph.Rcheck\00install.out 2>&1 && cp NCIgraph.Rcheck\00install.out NCIgraph-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=NCIgraph.buildbin-libdir --install="check:NCIgraph-install.out" --force-multiarch --no-vignettes --timings NCIgraph_1.16.0.tar.gz
StartedAt: 2015-10-09 04:21:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:23:27 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 106.2 seconds
RetCode: 0
Status:  OK  
CheckDir: NCIgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf NCIgraph.buildbin-libdir NCIgraph.Rcheck && mkdir NCIgraph.buildbin-libdir NCIgraph.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NCIgraph.buildbin-libdir NCIgraph_1.16.0.tar.gz >NCIgraph.Rcheck\00install.out 2>&1 && cp NCIgraph.Rcheck\00install.out NCIgraph-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=NCIgraph.buildbin-libdir --install="check:NCIgraph-install.out" --force-multiarch --no-vignettes --timings NCIgraph_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/NCIgraph.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NCIgraph/DESCRIPTION' ... OK
* this is package 'NCIgraph' version '1.16.0'
* 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph'
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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [14s] OK
** running examples for arch 'x64' ... [15s] 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/NCIgraph.Rcheck/00check.log'
for details.


NCIgraph.Rcheck/00install.out:


install for i386

* installing *source* package 'NCIgraph' ...
** R
** data
** 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 'NCIgraph' ...
** 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 'NCIgraph' as NCIgraph_1.16.0.zip
* DONE (NCIgraph)

NCIgraph.Rcheck/examples_i386/NCIgraph-Ex.timings:

nameusersystemelapsed
NCI.demo.cyList0.280.000.28
getNCIPathways3.880.023.90
getSubtype.NCIgraph404
parseNCInetwork0.260.000.26
translateNCI2GeneID3.980.003.98

NCIgraph.Rcheck/examples_x64/NCIgraph-Ex.timings:

nameusersystemelapsed
NCI.demo.cyList0.300.000.29
getNCIPathways4.410.004.61
getSubtype.NCIgraph4.040.004.04
parseNCInetwork0.260.000.27
translateNCI2GeneID4.120.014.13