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 '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
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)