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BioC 3.4: CHECK report for graphite on morelia

This page was generated on 2017-04-15 16:23:47 -0400 (Sat, 15 Apr 2017).

Package 558/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.20.1
Gabriele Sales
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/graphite
Last Changed Rev: 122747 / Revision: 128728
Last Changed Date: 2016-10-18 07:37:21 -0400 (Tue, 18 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: graphite
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.20.1.tar.gz
StartedAt: 2017-04-15 03:14:32 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 03:21:06 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 393.7 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_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/graphite.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.1’
* 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 123.193  1.648 125.063
runClipper       19.887  0.454  27.680
runSPIA           5.347  0.545  77.059
* 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-3.4-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.DeprecatedPathwayList1.9580.3383.076
as.list.PathwayList0.1610.0310.288
buildPathway0.0080.0010.015
convertIdentifiers0.8880.0201.372
cytoscapePlot0.0010.0000.001
pathwayDatabases0.0200.0010.031
pathwayGraph0.0470.0000.049
pathways0.0010.0000.001
runClipper19.887 0.45427.680
runClipperMulti123.193 1.648125.063
runDEGraph0.0020.0000.007
runDEGraphMulti0.0020.0000.002
runSPIA 5.347 0.54577.059
runTopologyGSA1.0280.0241.932
runTopologyGSAMulti0.7170.0210.739