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BioC 3.2: CHECK report for GraphPAC on perceval

This page was generated on 2015-11-10 14:47:52 -0800 (Tue, 10 Nov 2015).

Package 465/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphPAC 1.12.0
Gregory Ryslik
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GraphPAC
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / 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 UNNEEDED, same version exists in internal repository

Summary

Package: GraphPAC
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphPAC_1.12.0.tar.gz
StartedAt: 2015-11-10 05:41:49 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 05:43:59 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 130.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphPAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphPAC_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GraphPAC.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.12.0’
* 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 ... [10s/11s] 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:
  ‘igraph’ ‘iPAC’ ‘RMallow’ ‘TSP’
  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 ‘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 ‘vcount’
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’
* 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 ... [15s/16s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Find.TSP.Path 9.602  0.331  11.166
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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-3.2-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 9.602 0.33111.166
GraphClust0.0010.0010.001
Plot.Protein0.0010.0000.001
graphPAC-package0.0010.0000.001