RNAither 1.7.1
Nora Rieber
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither | | Last Changed Rev: 43413 / Revision: 43434 | | Last Changed Date: 2009-12-05 07:19:56 -0800 (Sat, 05 Dec 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/RNAither.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-30 r50622)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '1.7.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RNAither' 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in 'RNAither-Ex.R' failed.
The error most likely occurred in:
> ### * LiWongRank
>
> flush(stderr()); flush(stdout())
>
> ### Name: LiWongRank
> ### Title: Li Wong rank / invariant probeset normalization
> ### Aliases: LiWongRank
> ### Keywords: manip
>
> ### ** Examples
>
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
>
> normres <- LiWongRank(header, dataset, list("SigIntensity", "GeneName"))
Plate type 1 - Set a threshold to print out invariant probe set genes
c1 c2
[1,] NA NA
[2,] NA NA
[3,] NA NA
[4,] NA NA
[5,] NA NA
[6,] NA NA
[7,] NA NA
[8,] NA NA
[9,] NA NA
[10,] NA NA
[11,] NA NA
[12,] NA NA
[13,] NA NA
[14,] NA NA
[15,] NA NA
[16,] NA NA
[17,] NA NA
[18,] NA NA
Choose one gene for normalization - Input row number above.
Error in `[[<-.data.frame`(`*tmp*`, get("col4val"), value = numeric(0)) :
replacement has 0 rows, data has 24
Calls: LiWongRank -> [[<- -> [[<-.data.frame
Execution halted
* install options are ' --no-html'
* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.83) loaded.
To cite, see citation("SparseM")
Attaching package: 'SparseM'
The following object(s) are masked from package:stats :
model.response
The following object(s) are masked from package:base :
backsolve,
chol
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
pcaPP 0.1-1 loaded
Scalable Robust Estimators with High Breakdown Point (version 1.0-00)
** help
*** installing help indices
** building package indices ...
* DONE (RNAither)