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BioC 3.5: CHECK report for graphite on tokay2

This page was generated on 2017-08-16 13:21:16 -0400 (Wed, 16 Aug 2017).

Package 591/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.22.0
Gabriele Sales
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/graphite
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ TIMEOUT ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graphite
Version: 1.22.0
Command: rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.22.0.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.22.0.tar.gz
StartedAt: 2017-08-16 00:19:17 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:59:17 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 2400.7 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: graphite.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf graphite.buildbin-libdir graphite.Rcheck && mkdir graphite.buildbin-libdir graphite.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=graphite.buildbin-libdir graphite_1.22.0.tar.gz >graphite.Rcheck\00install.out 2>&1 && cp graphite.Rcheck\00install.out graphite-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=graphite.buildbin-libdir --install="check:graphite-install.out" --force-multiarch --no-vignettes --timings graphite_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/graphite.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'DEGraph' 'RCytoscape' 'RCy3'
* 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 'graphite' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 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 ... NOTE
Package unavailable to check Rd xrefs: 'DEGraph'
* 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 ... NOTE
  Note: found 26 marked UTF-8 strings
* 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' ...

graphite.Rcheck/00install.out:


install for i386

* installing *source* package 'graphite' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'graphite' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graphite' as graphite_1.22.0.zip
* DONE (graphite)

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

nameusersystemelapsed
as.list.DeprecatedPathwayList1.560.251.81
as.list.PathwayList0.110.000.11
buildPathway000
convertIdentifiers0.980.002.26
cytoscapePlot000
pathwayDatabases0.010.000.02
pathwayGraph0.060.000.06
pathways000
runClipper16.38 0.5816.95