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BioC 3.0: CHECK report for ToPASeq on oaxaca

This page was generated on 2015-04-10 10:09:29 -0700 (Fri, 10 Apr 2015).

Package 892/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToPASeq 1.0.1
Ivana Ihnatova
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/ToPASeq
Last Changed Rev: 96714 / Revision: 102249
Last Changed Date: 2014-11-13 00:09:28 -0800 (Thu, 13 Nov 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: ToPASeq
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ToPASeq_1.0.1.tar.gz
StartedAt: 2015-04-10 03:53:20 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:02:17 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 537.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ToPASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ToPASeq_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ToPASeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToPASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToPASeq’ version ‘1.0.1’
* 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 ‘ToPASeq’ can be installed ... [45s/47s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' calls in package code:
  ‘DEGraph’ ‘Rgraphviz’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SPIA: no visible binding for global variable ‘defaultEdgeAttrs’
plotCliques: no visible global function definition for ‘layoutGraph’
plotGraphW: no visible binding for global variable ‘defaultEdgeAttrs’
plotGraphW: no visible global function definition for ‘layoutGraph’
plotGraphW: no visible global function definition for ‘renderGraph’
plotRagraph : .local: no visible binding for global variable
  ‘drawAgNode’
plotRagraph : .local: no visible global function definition for
  ‘graphLayout’
plotRagraph : .local: no visible global function definition for
  ‘upRight’
plotRagraph : .local: no visible global function definition for
  ‘boundBox’
plotRagraph : .local: no visible global function definition for
  ‘botLeft’
plotRagraph : .local: no visible global function definition for ‘getX’
plotRagraph : .local: no visible global function definition for ‘getY’
plotRagraph : .local: no visible global function definition for
  ‘AgNode’
plotRagraph : .local: no visible global function definition for
  ‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeLW’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘getNodeHeight’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘labelText’
plotRagraph : .local : <anonymous>: no visible global function
  definition for ‘txtLabel’
plotRagraph : .local: no visible global function definition for
  ‘AgEdge’
prepareSPIA2: no visible binding for global variable ‘defaultEdgeAttrs’
renderSpline: no visible global function definition for ‘bezierPoints’
runDEGraphSigned : <anonymous>: no visible binding for global variable
  ‘defaultEdgeAttrs’
runDEGraphSigned : <anonymous>: no visible global function definition
  for ‘testOneGraph’
runSPIA: no visible binding for global variable ‘defaultEdgeAttrs’
runTopologyGSADirected: no visible binding for global variable ‘name’
* 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 ... [46s/48s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Clipper 15.343  0.238   16.03
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/30s]
 [29s/30s] 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ToPASeq.Rcheck/00check.log’
for details.

ToPASeq.Rcheck/00install.out:

* installing *source* package ‘ToPASeq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ToPASeq)

ToPASeq.Rcheck/ToPASeq-Ex.timings:

nameusersystemelapsed
AdjacencyMatrix2Pathway0.0370.0010.038
Clipper15.343 0.23816.030
DEGraph1.8200.0843.257
PWEA0.0010.0000.002
SPIA0.8360.0160.855
TAPPA1.3590.0211.383
TBS1.8900.0311.925
ToPASeq-package0.0020.0010.001
TopologyGSA0.0010.0000.002
convertIdentifiersByVector0.0040.0000.005
defaultEdgeAttrs0.0110.0000.012
graphNEL2Pathway0.0950.0010.096
reduceRraph1.8690.0091.883