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BioC 3.5: CHECK report for NetSAM on malbec2

This page was generated on 2017-08-16 13:15:06 -0400 (Wed, 16 Aug 2017).

Package 896/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetSAM 1.16.0
Bing Zhang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/NetSAM
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NetSAM
Version: 1.16.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NetSAM_1.16.0.tar.gz
StartedAt: 2017-08-16 00:58:45 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:59:55 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 70.5 seconds
RetCode: 0
Status:  OK 
CheckDir: NetSAM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NetSAM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/NetSAM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-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 ‘1.16.0’
* 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 ... 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 : transformFromWalktrapToHclust: no visible global function
  definition for ‘as.dendrogram’
NetSAM : transformFromWalktrapToHclust: no visible global function
  definition for ‘order.dendrogram’
NetSAM : evaluateWalktrapStep: no visible global function definition
  for ‘walktrap.community’
NetSAM : evaluateWalktrapStep: no visible global function definition
  for ‘as.dist’
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 : identifySig: no visible global function definition for ‘sd’
NetSAM : identifySig: no visible global function definition for ‘pnorm’
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’
NetSAM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  V add.edges as.dendrogram as.dist clusters degree.sequence.game
  ecount get.adjacency get.edgelist get_order graph.edgelist
  igraph.from.graphNEL induced.subgraph order.dendrogram pnorm
  read.graph sd seriate simplify vcount walktrap.community write.table
Consider adding
  importFrom("stats", "as.dendrogram", "as.dist", "order.dendrogram",
             "pnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
NetSAM 10.584  0.048  10.683
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/home/biocbuild/bbs-3.5-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
NetSAM10.584 0.04810.683