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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetSAM_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/NetSAM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 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
NetSAM 9.384 0.086 9.673
* 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
‘/Users/biocbuild/bbs-3.5-bioc/meat/NetSAM.Rcheck/00check.log’
for details.
* 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)