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BioC 3.0: CHECK report for CNORfeeder on zin1

This page was generated on 2015-04-10 09:40:43 -0700 (Fri, 10 Apr 2015).

Package 176/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORfeeder 1.6.0
F.Eduati
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CNORfeeder
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CNORfeeder
Version: 1.6.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CNORfeeder_1.6.0.tar.gz
StartedAt: 2015-04-09 22:44:55 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:45:57 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 62.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CNORfeeder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CNORfeeder_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/CNORfeeder.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORfeeder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORfeeder’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNORfeeder’ can be installed ... [5s/5s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘catnet’ ‘igraph’ ‘minet’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘graph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Binference: no visible global function definition for ‘cnSearchSA’
Binference: no visible global function definition for ‘cnMatEdges’
MIinference: no visible global function definition for ‘build.mim’
MIinference: no visible global function definition for ‘aracne’
MIinference: no visible global function definition for ‘clr’
mapBTables2model: no visible global function definition for ‘nodes’
searchLinkGraph: no visible global function definition for ‘nodes’
searchLinkGraph: no visible global function definition for ‘removeNode’
searchPPIigraph: no visible global function definition for ‘V’
searchPPIigraph: no visible global function definition for
  ‘induced.subgraph’
searchPPIigraph: no visible global function definition for
  ‘get.shortest.paths’
weighting: no visible global function definition for ‘is.igraph’
* 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 ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [4s/4s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/CNORfeeder.Rcheck/00check.log’
for details.

CNORfeeder.Rcheck/00install.out:

* installing *source* package ‘CNORfeeder’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORfeeder)

CNORfeeder.Rcheck/CNORfeeder-Ex.timings:

nameusersystemelapsed
Binference0.6960.0120.545
CNORfeeder-package0.8280.0040.832
MIinference0.3280.0120.342
gaBinaryT1W0.5760.0080.587
linksRanking0.0440.0000.047
makeBTables0.0320.0000.032
mapBTables2model0.5600.0080.568
mapDDN2model1.0600.0160.882
weighting0.6000.0080.608