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Package 30/264HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.5.7
Jan Oosting
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarraySNP
Last Changed Rev: 30821 / Revision: 30951
Last Changed Date: 2008-04-03 08:26:56 -0700 (Thu, 03 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: beadarraySNP
Version: 1.5.7
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check beadarraySNP_1.5.7.tar.gz
StartedAt: 2008-04-09 05:25:51 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 05:27:23 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 92.1 seconds
RetCode: 0
Status: WARNINGS
CheckDir: beadarraySNP.Rcheck
Warnings: 3

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.5.7'
* 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 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 ... OK
* checking Rd files ... WARNING
Rd files without 'description':
  reportGenotypeSegmentation.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  calculateLair
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 'GenomicReports':
reportChromosomesSmoothCopyNumber
  Code: function(snpdata, grouping, normalizedTo = 2, smooth.lambda =
                 2, ridge.kappa = 0, plotLOH = c("none", "marker",
                 "line", "NorTum"), sample.colors = NULL, ideo.bleach =
                 0.25, ...)
  Docs: function(snpdata, grouping, normalizedTo = 2, smooth.lambda =
                 2, ridge.kappa = 0, plotLOH = c("none", "marker",
                 "line", "NorTum"), sample.colors = NULL, ...)
  Argument names in code not in docs:
    ideo.bleach
  Mismatches in argument names:
    Position: 8 Code: ideo.bleach Docs: ...

Codoc mismatches from documentation object 'read.SnpSetIllumina':
read.SnpSetIllumina
  Code: function(samplesheet, manifestpath = NULL, reportpath = NULL,
                 rawdatapath = NULL, reportfile = NULL, briefOPAinfo =
                 TRUE, readTIF = FALSE, ...)
  Docs: function(samplesheet, manifestpath = NULL, reportpath = NULL,
                 rawdatapath = NULL, reportfile = NULL, briefOPAinfo =
                 TRUE, verbose = FALSE, readTIF = FALSE, ...)
  Argument names in docs not in code:
    verbose
  Mismatches in argument names:
    Position: 7 Code: readTIF Docs: verbose
    Position: 8 Code: ... 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 using pdflatex ... OK

WARNING: There were 3 warnings, see
  E:/biocbld/bbs-2.2-bioc/meat/beadarraySNP.Rcheck/00check.log
for details

beadarraySNP.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/beadarraySNP.Rcheck


---------- Making package beadarraySNP ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing data files
  preparing package beadarraySNP 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
Loading required package: lodplot
Loading required package: grid
  installing man source files
  installing indices
  not zipping data
  installing help
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 >>> Building/Updating help pages for package 'beadarraySNP'
     Formats: text html latex example chm 
  BeadstudioQC                      text    html    latex           chm
  CopynumberConversion              text    html    latex           chm
  Datasets                          text    html    latex           chm
  GenomicReports                    text    html    latex   example chm
  PolarTransforms                   text    html    latex   example chm
  QCIllumina-class                  text    html    latex           chm
  Sample_Map2Samplesheet            text    html    latex           chm
  alterCN                           text    html    latex           chm
  arrayType                         text    html    latex           chm
  backgroundCorrect.SNP             text    html    latex   example chm
  backgroundEstimate                text    html    latex           chm
  calculateLOH                      text    html    latex           chm
  calculateQCarray                  text    html    latex   example chm
  class.SnpSetIllumina              text    html    latex           chm
  compareGenotypes                  text    html    latex   example chm
  createCNSummary                   text    html    latex           chm
  getDNAindex                       text    html    latex           chm
  heterozygosity                    text    html    latex   example chm
  heterozygousSNPs                  text    html    latex   example chm
  interactiveCNselect               text    html    latex           chm
  normalizeBetweenAlleles.SNP       text    html    latex   example chm
  normalizeLoci.SNP                 text    html    latex   example chm
  normalizeWithinArrays.SNP         text    html    latex   example chm
  pdfChromosomesSmoothCopyNumber    text    html    latex   example chm
  pdfQC                             text    html    latex           chm
  plotGoldenGate4OPA                text    html    latex           chm
  plotQC                            text    html    latex   example chm
  read.SnpSetIllumina               text    html    latex   example chm
  removeLowQualityProbes            text    html    latex           chm
  removeLowQualitySamples           text    html    latex   example chm
  renameOPA                         text    html    latex           chm
  reportGenotypeSegmentation        text    html    latex           chm
  reportSamplePanelQC-methods       text    html    latex   example chm
  segmentate                        text    html    latex           chm
  setRealCN                         text    html    latex           chm
  smoothed.intensity                text    html    latex           chm
  standardNormalization             text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.2-bioc\meat\beadarraySNP.Rcheck\00_pkg_src\beadarraySNP\chm\beadarraySNP.chm


Compile time: 0 minutes, 1 second
38	Topics
187	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.2-bioc\meat\beadarraySNP.Rcheck\00_pkg_src\beadarraySNP\chm\beadarraySNP.chm, 56,135 bytes
Compression decreased file by 76,377 bytes.
  adding MD5 sums

* DONE (beadarraySNP)