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BioC 3.5: CHECK report for GraphPAC on oaxaca

This page was generated on 2017-03-04 16:44:59 -0500 (Sat, 04 Mar 2017).

Package 572/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphPAC 1.17.0
Gregory Ryslik
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GraphPAC
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: GraphPAC
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphPAC_1.17.0.tar.gz
StartedAt: 2017-03-04 04:02:21 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:04:24 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 123.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphPAC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphPAC_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GraphPAC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GraphPAC’ version ‘1.17.0’
* 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 ‘GraphPAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RMallow’ ‘TSP’ ‘iPAC’ ‘igraph’
  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
Find.TSP.Path: no visible global function definition for ‘dist’
Find.TSP.Path: no visible global function definition for ‘ATSP’
Find.TSP.Path: no visible global function definition for ‘insert_dummy’
Find.TSP.Path: no visible global function definition for ‘solve_TSP’
Find.TSP.Path: no visible global function definition for ‘cut_tour’
GraphClust: no visible global function definition for ‘graph.empty’
GraphClust: no visible global function definition for ‘V’
GraphClust: no visible global function definition for ‘V<-’
GraphClust: no visible global function definition for ‘add.edges’
GraphClust: no visible global function definition for ‘nmc’
Plot.Protein: no visible global function definition for ‘heat.colors’
Plot.Protein: no visible global function definition for ‘vcount’
Plot.Protein: no visible global function definition for ‘gray’
Plot.Protein: no visible global function definition for ‘topo.colors’
Plot.Protein: no visible global function definition for ‘cm.colors’
Plot.Protein: no visible global function definition for ‘V’
Plot.Protein: no visible global function definition for ‘tkplot’
Plot.Protein: no visible binding for global variable ‘layout.circle’
Undefined global functions or variables:
  ATSP V V<- add.edges cm.colors cut_tour dist graph.empty gray
  heat.colors insert_dummy layout.circle nmc solve_TSP tkplot
  topo.colors vcount
Consider adding
  importFrom("grDevices", "cm.colors", "gray", "heat.colors",
             "topo.colors")
  importFrom("stats", "dist")
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 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
Find.TSP.Path 5.787   0.39  13.708
* 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/GraphPAC.Rcheck/00check.log’
for details.


GraphPAC.Rcheck/00install.out:

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

GraphPAC.Rcheck/GraphPAC-Ex.timings:

nameusersystemelapsed
Find.TSP.Path 5.787 0.39013.708
GraphClust000
Plot.Protein0.0010.0000.000
graphPAC-package0.0000.0000.001