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 |
* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* 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 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 ... 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
/home/biocbuild/bbs-2.2-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 (0.77) loaded. To cite, see citation("SparseM")
Loading required package: lodplot
Loading required package: grid
** help
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \value
Note: removing empty section \note
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \references
>>> Building/Updating help pages for package 'beadarraySNP'
Formats: text html latex example
BeadstudioQC text html latex
CopynumberConversion text html latex
Datasets text html latex
GenomicReports text html latex example
PolarTransforms text html latex example
QCIllumina-class text html latex
Sample_Map2Samplesheet text html latex
alterCN text html latex
arrayType text html latex
backgroundCorrect.SNP text html latex example
backgroundEstimate text html latex
calculateLOH text html latex
calculateQCarray text html latex example
class.SnpSetIllumina text html latex
compareGenotypes text html latex example
createCNSummary text html latex
getDNAindex text html latex
heterozygosity text html latex example
heterozygousSNPs text html latex example
interactiveCNselect text html latex
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
plotGoldenGate4OPA 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
reportGenotypeSegmentation text html latex
reportSamplePanelQC-methods text html latex example
segmentate text html latex
setRealCN text html latex
smoothed.intensity text html latex
standardNormalization text html latex example
** building package indices ...
* DONE (beadarraySNP)