Back to the "Multiple platform build/check report"
| IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
| Package 29/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
beadarraySNP1.3.7Jan OostingLast Changed Date: 2007-07-26 08:38:57 -0700 Last Changed Rev: 25976 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
| wellington | Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | [ WARNINGS ] | OK | |
| pitt | Mac OS X (10.4.10) | i386 | OK | WARNINGS | OK |
| Package: beadarraySNP |
| Version: 1.3.7 |
| Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check beadarraySNP_1.3.7.tar.gz |
| RetCode: 0 |
| Time: 93.8 seconds |
| Status: WARNINGS |
| CheckDir: beadarraySNP.Rcheck |
| Warnings: 2 |
* checking for working latex ... OK
* using log directory 'E:/biocbld/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 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
E:/biocbld/bbs-2.1-bioc/meat/beadarraySNP.Rcheck/00check.log
for details
beadarraySNP.Rcheck/00install.out:
installing R.css in E:/biocbld/bbs-2.1-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
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'backgroundEstimate' on or after line 50
Note: unmatched right brace in 'backgroundEstimate.Rd' on or after line 50
Note: unmatched right brace in 'class.SnpSetIllumina' on or after line 133
Note: unmatched right brace in 'class.SnpSetIllumina.Rd' on or after line 133
Note: unmatched right brace in 'heterozygousSNPs' on or after line 57
Note: unmatched right brace in 'heterozygousSNPs.Rd' on or after line 57
Note: unmatched right brace in 'read.SnpSetIllumina' on or after line 80
Note: unmatched right brace in 'read.SnpSetIllumina.Rd' on or after line 80
Note: unmatched right brace in 'smoothed.intensity' on or after line 21
Note: unmatched right brace in 'smoothed.intensity.Rd' on or after line 21
>>> Building/Updating help pages for package 'beadarraySNP'
Formats: text html latex example chm
CopynumberConversion text html latex example chm
Datasets text html latex chm
GenomicReports text html latex example chm
PolarTransforms text html latex example chm
QCIllumina-class text html latex chm
arrayType text html latex chm
backgroundCorrect.SNP text html latex example chm
backgroundEstimate text html latex example chm
calculateLOH text html latex example chm
calculateQCarray text html latex example chm
class.SnpSetIllumina text html latex chm
compareGenotypes text html latex example chm
heterozygosity text html latex example chm
heterozygousSNPs text html latex example 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
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 example chm
reportSamplePanelQC-methods text html latex example chm
smoothed.intensity text html latex example chm
standardNormalization text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.1-bioc\meat\beadarraySNP.Rcheck\00_pkg_src\beadarraySNP\chm\beadarraySNP.chm
Compile time: 0 minutes, 0 seconds
28 Topics
131 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.1-bioc\meat\beadarraySNP.Rcheck\00_pkg_src\beadarraySNP\chm\beadarraySNP.chm, 48,395 bytes
Compression decreased file by 56,360 bytes.
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
adding MD5 sums
* DONE (beadarraySNP)