R Development Page

spiderDev log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2016-04-01-12-24/RF_PKG_CHECK/PKGS/spiderDev.Rcheck'
* using R version 3.2.4 Patched (2016-03-28 r70391)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'spiderDev/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spiderDev' version '0.0-10'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Samuel Brown '
New submission

The Title field should be in title case, current version then in title case:
'Species Identity and Evolution in R--development'
'Species Identity and Evolution in R--Development'

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 whether package 'spiderDev' can be installed ... OK
* checking installed package size ... OK
* checking package 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'XML' 'phangorn'
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.simRFLP
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DNAbin2alignment: no visible global function definition for 'write.dna'
DNAbin2alignment: no visible global function definition for
  'read.alignment'
IDunknown: no visible global function definition for 'bind'
IDunknown: no visible global function definition for 'dist.dna'
baseContent: no visible global function definition for 'base.freq'
exCon: no visible global function definition for 'dist.dna'
giveMeThePicture : : no visible global function definition
  for 'dist.dna'
inCon: no visible global function definition for 'dist.dna'
nodeRect: no visible binding for global variable '.PlotPhyloEnv'
nucDiagExptl: no visible global function definition for 'seg.sites'
phylo2MRP: no visible global function definition for 'prop.part'
pindel: no visible global function definition for 'dist.dna'
satPlot: no visible global function definition for 'dist.dna'
satPlot: no visible global function definition for 'nj'
satPlot: no visible global function definition for 'as.phyDat'
satPlot: no visible global function definition for 'pml'
satPlot: no visible global function definition for 'optim.pml'
satPlot2: no visible global function definition for 'dist.dna'
search.GB: no visible global function definition for 'xmlTreeParse'
search.GB: no visible global function definition for 'getNodeSet'
search.GB: no visible binding for global variable 'xmlValue'
search.GB: no visible global function definition for 'xmlNode'
search.GB: no visible global function definition for 'append.xmlNode'
search.GB : : no visible global function definition for
  'as.DNAbin'
search.GB : : no visible global function definition for
  'xmlValue'
seeSegSites: no visible global function definition for 'seg.sites'
simRFLP: no visible binding for global variable 'enzymes'
sisterMatrix: no visible global function definition for 'vcv'
sppEdge: no visible global function definition for 'mrca'

Found the following calls to data() loading into the global environment:
File 'spiderDev/R/simRFLP.R':
  data(enzymes, package = "spiderDev")
See section 'Good practice' in '?data'.
* checking Rd files ... NOTE
prepare_Rd: AICgmyc.Rd:46-48: Dropping empty section \note
prepare_Rd: DNAccf.Rd:36-38: Dropping empty section \note
prepare_Rd: IDunknown.Rd:32-34: Dropping empty section \note
prepare_Rd: baseContent.Rd:16-17: Dropping empty section \details
prepare_Rd: baseContent.Rd:28-30: Dropping empty section \note
prepare_Rd: best2nullLRT.Rd:38-40: Dropping empty section \note
prepare_Rd: branches.per.tip.Rd:17-18: Dropping empty section \details
prepare_Rd: branches.per.tip.Rd:28-30: Dropping empty section \note
prepare_Rd: branchesFromNode.Rd:18-19: Dropping empty section \details
prepare_Rd: branchesFromNode.Rd:29-31: Dropping empty section \note
prepare_Rd: clustCI.gmyc.Rd:37-39: Dropping empty section \note
prepare_Rd: clustCI.gmyc.Rd:29-30: Dropping empty section \references
prepare_Rd: clustGMYC.Rd:18-19: Dropping empty section \details
prepare_Rd: clustGMYC.Rd:33-35: Dropping empty section \note
prepare_Rd: clustGMYC.Rd:25-26: Dropping empty section \references
prepare_Rd: col2string.Rd:17-18: Dropping empty section \details
prepare_Rd: col2string.Rd:32-34: Dropping empty section \note
prepare_Rd: col2string.Rd:24-25: Dropping empty section \references
prepare_Rd: compList.Rd:33-35: Dropping empty section \note
prepare_Rd: compList.Rd:39-41: Dropping empty section \seealso
prepare_Rd: compVectorDist.Rd:35-37: Dropping empty section \note
prepare_Rd: exCon.Rd:44-46: Dropping empty section \note
prepare_Rd: homoP.Rd:30-32: Dropping empty section \note
prepare_Rd: homoP.Rd:36-38: Dropping empty section \seealso
prepare_Rd: narrowingWindow.Rd:37-39: Dropping empty section \note
prepare_Rd: narrowingWindow.Rd:43-45: Dropping empty section \seealso
prepare_Rd: nodeDesc.Rd:31-33: Dropping empty section \note
prepare_Rd: nodeRect.Rd:23-24: Dropping empty section \details
prepare_Rd: nodeRect.Rd:34-36: Dropping empty section \note
prepare_Rd: nodeRect.Rd:40-41: Dropping empty section \seealso
prepare_Rd: permDNA.Rd:18-20: Dropping empty section \details
prepare_Rd: permDNA.Rd:30-32: Dropping empty section \note
prepare_Rd: permDNA.Rd:24-26: Dropping empty section \references
prepare_Rd: permDNA.Rd:36-38: Dropping empty section \seealso
prepare_Rd: phylo2MRP.Rd:17-18: Dropping empty section \details
prepare_Rd: phylo2MRP.Rd:28-30: Dropping empty section \note
prepare_Rd: phylo2MRP.Rd:34-35: Dropping empty section \seealso
prepare_Rd: pindel.Rd:19-20: Dropping empty section \details
prepare_Rd: pindel.Rd:34-36: Dropping empty section \note
prepare_Rd: pindel.Rd:26-27: Dropping empty section \references
prepare_Rd: pindel.Rd:45-47: Dropping empty section \examples
prepare_Rd: plot.simRFLP.Rd:35-37: Dropping empty section \note
prepare_Rd: plot.simRFLP.Rd:29-31: Dropping empty section \references
prepare_Rd: screeline.Rd:17-18: Dropping empty section \details
prepare_Rd: screeline.Rd:31-33: Dropping empty section \note
prepare_Rd: seeSegSites.Rd:17-18: Dropping empty section \details
prepare_Rd: simRFLP.Rd:32-34: Dropping empty section \note
prepare_Rd: sppEdge.Rd:31-33: Dropping empty section \note
prepare_Rd: tclust2sppVector.Rd:17-19: Dropping empty section \details
prepare_Rd: tclust2sppVector.Rd:21-22: Dropping empty section \value
prepare_Rd: tclust2sppVector.Rd:28-30: Dropping empty section \note
prepare_Rd: tipToRootDist.Rd:17-18: Dropping empty section \details
prepare_Rd: tipToRootDist.Rd:28-30: Dropping empty section \note
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'sppEdge.Rd':
  \examples lines wider than 100 characters:
     anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"),  function(x) paste(x[1], x[2], sep="_"))

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'DNAbin2alignment' 'correctAlignment' 'sisterMatrix' 'termBL'
  'termBalance'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'nodeRect':
nodeRect
  Code: function(start, end = NULL, node, width = 0.05, lty = 1, col =
                 "blue", border = "blue", lwd = 1)
  Docs: function(start, end = NULL, node, width = 0.05, lty = 1, col =
                 "blue", lwd = 1)
  Argument names in code not in docs:
    border
  Mismatches in argument names:
    Position: 7 Code: border Docs: lwd

* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
satPlot         30.10   0.04   30.28
compVectorDist  17.47   0.00   17.48
narrowingWindow  7.43   0.67    8.14
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 7 NOTEs
See
  'R:/run/building/build_2016-04-01-12-24/RF_PKG_CHECK/PKGS/spiderDev.Rcheck/00check.log'
for details.


Run time: 175.97 seconds.