Package: beadarraySNP

Version: 1.3.7

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check beadarraySNP_1.3.7.tar.gz

RetCode: 0

Time: 231.5 seconds

Status: WARNINGS

CheckDir: beadarraySNP.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.3.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarraySNP' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
segmentate: no visible binding for global variable 'sorted.sl'
setRealCN: no visible binding for global variable 'smp'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  alterCN createCNSummary getDNAindex getIdGoldenGate4OPA
  interactiveCNselect plotGoldenGate4OPA reportGenotypeSegmentation
  segmentate setRealCN
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'copynumberConversion':
convert2aCGH
  Code: function(object, normalizedTo = 2, doLog = TRUE, organism =
                 "hsa")
  Docs: function(object, normalizedTo = 2, organism = "hsa")
  Argument names in code not in docs:
    doLog
  Mismatches in argument names:
    Position: 3 Code: doLog Docs: organism
convert2SegList
  Code: function(object, normalizedTo = 2, doLog = TRUE, organism =
                 "hsa")
  Docs: function(object, normalizedTo = 2, organism = "hsa")
  Argument names in code not in docs:
    doLog
  Mismatches in argument names:
    Position: 3 Code: doLog Docs: organism

Codoc mismatches from documentation object 'GenomicReports':
reportSamplesSmoothCopyNumber
  Code: function(snpdata, grouping, normalizedTo = 2, smooth.lambda =
                 2, ridge.kappa = 0, plotLOH = c("none", "marker",
                 "line", "NorTum"), sample.colors = NULL, ...)
  Docs: function(snpdata, grouping, normalizedTo = 2, smooth.lambda =
                 2, ridge.kappa = 0, plotLOH = c("none", "marker",
                 "line", "NorTum"), ...)
  Argument names in code not in docs:
    sample.colors
  Mismatches in argument names:
    Position: 7 Code: sample.colors Docs: ...
reportGenomeGainLossLOH
  Code: function(snpdata, grouping, plotSampleNames = FALSE,
                 sizeSampleNames = 4, distance.min, upcolor = "red",
                 downcolor = "blue", lohcolor = "grey", hetcolor =
                 "lightgrey", lohwidth = 1, segment = 101, orientation
                 = c("V", "H"), ...)
  Docs: function(snpdata, grouping, plotSampleNames = FALSE,
                 distance.min, upcolor = "red", downcolor = "blue",
                 lohcolor = "grey", hetcolor = "lightgrey", lohwidth =
                 1, segment = 101, orientation = c("V", "H"), ...)
  Argument names in code not in docs:
    sizeSampleNames
  Mismatches in argument names (first 3):
    Position: 4 Code: sizeSampleNames Docs: distance.min
    Position: 5 Code: distance.min Docs: upcolor
    Position: 6 Code: upcolor Docs: downcolor

Codoc mismatches from documentation object 'read.SnpSetIllumina':
read.SnpSetIllumina
  Code: function(samplesheet, manifestpath = NULL, reportpath = NULL,
                 rawdatapath = NULL, reportfile = NULL, briefOPAinfo =
                 TRUE, verbose = FALSE, readTIF = FALSE, ...)
  Docs: function(samplesheet, manifestpath = NULL, reportpath = NULL,
                 rawdatapath = NULL, reportfile = NULL, briefOPAinfo =
                 TRUE, verbose = FALSE)
  Argument names in code not in docs:
    readTIF ...

* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating beadarraySNP-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating beadarraySNP-manual.tex ... OK
* checking beadarraySNP-manual.tex ... OK

WARNING: There were 2 warnings, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/beadarraySNP.Rcheck/00check.log
for details

* Installing *source* package 'beadarraySNP' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: tools
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM
Package SparseM (0.73) loaded.  To cite, see citation("SparseM")
Loading required package: lodplot
Loading required package: grid
** help
Note: unmatched right brace in 'backgroundEstimate' on or after line 50
Note: unmatched right brace in 'class.SnpSetIllumina' on or after line 133
Note: unmatched right brace in 'heterozygousSNPs' on or after line 57
Note: unmatched right brace in 'read.SnpSetIllumina' on or after line 80
Note: unmatched right brace in 'smoothed.intensity' on or after line 21
 >>> Building/Updating help pages for package 'beadarraySNP'
     Formats: text html latex example 
  CopynumberConversion              text    html    latex   example
  Datasets                          text    html    latex
  GenomicReports                    text    html    latex   example
  PolarTransforms                   text    html    latex   example
  QCIllumina-class                  text    html    latex
  arrayType                         text    html    latex
  backgroundCorrect.SNP             text    html    latex   example
  backgroundEstimate                text    html    latex   example
  calculateLOH                      text    html    latex   example
  calculateQCarray                  text    html    latex   example
  class.SnpSetIllumina              text    html    latex
  compareGenotypes                  text    html    latex   example
  heterozygosity                    text    html    latex   example
  heterozygousSNPs                  text    html    latex   example
  normalizeBetweenAlleles.SNP       text    html    latex   example
  normalizeLoci.SNP                 text    html    latex   example
  normalizeWithinArrays.SNP         text    html    latex   example
  pdfChromosomesSmoothCopyNumber    text    html    latex   example
  pdfQC                             text    html    latex
  plotQC                            text    html    latex   example
  read.SnpSetIllumina               text    html    latex   example
  removeLowQualityProbes            text    html    latex
  removeLowQualitySamples           text    html    latex   example
  renameOPA                         text    html    latex   example
  reportSamplePanelQC-methods       text    html    latex   example
  smoothed.intensity                text    html    latex   example
  standardNormalization             text    html    latex   example
** building package indices ...
* DONE (beadarraySNP)