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BioC 3.0: CHECK report for NetSAM on zin1

This page was generated on 2015-04-10 09:40:58 -0700 (Fri, 10 Apr 2015).

Package 603/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetSAM 1.6.0
Bing Zhang
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/NetSAM
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: NetSAM
Version: 1.6.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings NetSAM_1.6.0.tar.gz
StartedAt: 2015-04-10 02:32:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:33:23 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 43.3 seconds
RetCode: 0
Status:  OK 
CheckDir: NetSAM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings NetSAM_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/NetSAM.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 ‘NetSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetSAM’ 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 ‘NetSAM’ can be installed ... [2s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘graph’ ‘igraph’ ‘seriation’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘igraph:::degree’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘NetSAM/R/zzz.R’:
  .onLoad calls:
    cat("******************************************\n")
    cat("*                                        *\n")
    cat("*         Welcome to use NetSAM !        *\n")
    cat("*                                        *\n")
    cat("******************************************\n")
    require(methods)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

******************************************
*                                        *
*         Welcome to use NetSAM !        *
*                                        *
******************************************
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
  definition for ‘V’
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
  definition for ‘add.edges’
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
  definition for ‘get.adjacency’
NetSAM : evaluateWalktrapStep: no visible global function definition
  for ‘walktrap.community’
NetSAM : evaluateWalktrapStep: no visible global function definition
  for ‘seriate’
NetSAM : evaluateWalktrapStep: no visible global function definition
  for ‘get_order’
NetSAM : identifySig: no visible global function definition for
  ‘degree.sequence.game’
NetSAM : identifySig: no visible global function definition for
  ‘walktrap.community’
NetSAM : identifyHierOr: no visible global function definition for
  ‘induced.subgraph’
NetSAM : createHMIFile: no visible global function definition for ‘V’
NetSAM: no visible global function definition for ‘read.graph’
NetSAM: no visible global function definition for ‘graph.edgelist’
NetSAM: no visible global function definition for
  ‘igraph.from.graphNEL’
NetSAM: no visible global function definition for ‘V’
NetSAM: no visible global function definition for ‘vcount’
NetSAM: no visible global function definition for ‘ecount’
NetSAM: no visible global function definition for ‘simplify’
NetSAM: no visible global function definition for ‘clusters’
NetSAM: no visible global function definition for ‘induced.subgraph’
NetSAM: no visible global function definition for ‘get.edgelist’
* 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 ... [8s/8s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
NetSAM 6.784  0.032   6.859
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/NetSAM.Rcheck/00check.log’
for details.

NetSAM.Rcheck/00install.out:

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

NetSAM.Rcheck/NetSAM-Ex.timings:

nameusersystemelapsed
NetSAM6.7840.0326.859