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BioC 3.1: CHECK report for graphite on petty

This page was generated on 2015-10-09 09:34:43 -0700 (Fri, 09 Oct 2015).

Package 437/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.14.1
Gabriele Sales
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/graphite
Last Changed Rev: 105077 / Revision: 109384
Last Changed Date: 2015-06-17 07:05:48 -0700 (Wed, 17 Jun 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: graphite
Version: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.14.1.tar.gz
StartedAt: 2015-10-08 23:30:45 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:38:53 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 488.1 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/graphite.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.14.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘graphite’ can be installed ... [35s/36s] OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
runTopologyGSA,list : .local: no visible binding for global variable
  ‘expr’
runTopologyGSA,list : .local: no visible binding for global variable
  ‘classes’
* 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 ... NOTE
  Note: found 32 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 ... [293s/298s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 233.111  4.049 237.353
runClipper       26.967  0.526  27.511
runSPIA           9.473  0.105  12.588
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘graphite’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (graphite)

graphite.Rcheck/graphite-Ex.timings:

nameusersystemelapsed
as.list.DeprecatedPathwayList2.4910.3602.854
as.list.PathwayList0.2110.0340.245
convertIdentifiers1.1100.0251.135
cytoscapePlot0.0010.0000.001
pathwayDatabases0.0410.0030.045
pathwayGraph0.0440.0010.045
pathways0.0010.0000.001
runClipper26.967 0.52627.511
runClipperMulti233.111 4.049237.353
runDEGraph2.7780.1223.294
runDEGraphMulti1.3350.0161.351
runSPIA 9.473 0.10512.588
runTopologyGSA2.4240.0363.649
runTopologyGSAMulti1.3880.0331.927