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BioC 3.5: CHECK report for graphite on oaxaca

This page was generated on 2017-03-04 16:41:45 -0500 (Sat, 04 Mar 2017).

Package 571/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.21.0
Gabriele Sales
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graphite
Last Changed Rev: 122746 / Revision: 127142
Last Changed Date: 2016-10-18 07:34:37 -0400 (Tue, 18 Oct 2016)
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  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: graphite
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.21.0.tar.gz
StartedAt: 2017-03-04 04:01:18 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:06:42 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 324.6 seconds
RetCode: 0
Status:  OK 
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/graphite.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... 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
* 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 28 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 130.269  1.784 141.379
runClipper       19.015  0.504  19.934
runSPIA           5.276  0.291  20.599
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/graphite.Rcheck/00check.log’
for details.


graphite.Rcheck/00install.out:

* 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
* DONE (graphite)

graphite.Rcheck/graphite-Ex.timings:

nameusersystemelapsed
as.list.DeprecatedPathwayList1.6650.2741.946
as.list.PathwayList0.1080.0230.141
buildPathway0.0050.0000.006
convertIdentifiers1.2200.0271.266
cytoscapePlot0.0000.0000.001
pathwayDatabases0.0140.0000.015
pathwayGraph0.0480.0000.049
pathways000
runClipper19.015 0.50419.934
runClipperMulti130.269 1.784141.379
runDEGraph0.0020.0000.001
runDEGraphMulti0.0010.0000.001
runSPIA 5.276 0.29120.599
runTopologyGSA1.1820.0211.251
runTopologyGSAMulti1.0670.0331.101