Package: RNAither

Version: 2.1.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.1.0.tar.gz

StartedAt: 2011-06-22 05:05:40 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 05:09:46 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 246.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: RNAither.Rcheck

Warnings: NA

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.1.0’
* 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 installed package size ... 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 ... NOTE
Found the following CITATION file(s) in a non-standard place:
  inst/extdata/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘RNAither-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gseaAnalysis
> ### Title: Perform a GSEA analysis of a list of genes
> ### Aliases: gseaAnalysis
> ### Keywords: database datagen
> 
> ### ** Examples
> 
> data(scoredDataset1, package="RNAither")
> data(pValVec1, package="RNAither")
> 
> ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.
> 
> scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Hits1", 0.1, 
+ "GeneName", "pvalue_testfile1.txt")
> hitVector1 <- scoredHits1[[2]]
> gseaTable <- gseaAnalysis(hitVector1, "biological_process")
Error in getBM(attributes = c("hgnc_symbol", goIDs), filters = "hgnc_symbol",  : 
  Invalid attribute(s): go_biological_process_id 
Please use the function 'listAttributes' to get valid attribute names
Calls: gseaAnalysis -> GOannotate -> getBM
Execution halted

* 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
  'browseVignettes()'. 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 (0.89) loaded.
	   To cite, see citation("SparseM")


Attaching package: ‘SparseM’

The following object(s) are masked from ‘package:base’:

    backsolve


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
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘vignetteRNAither.Rnw’ 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.081	0.006	0.088
DRQualControl	0.145	0.009	0.168
LiWongRank	0.331	0.004	0.339
MannWhitney	0.073	0.004	0.091
RankProduct	0.863	0.010	0.881
SNRQualControl	0.056	0.010	0.067
Ttest	0.074	0.003	0.079
ZPRIMEQualControl	0.067	0.011	0.097
ZScore	0.028	0.003	0.032
ZScorePerScreen	0.019	0.003	0.022
ZScorePlot	0.156	0.009	0.172
ZScorePlotTwo	0.049	0.006	0.061
channelPlot	0.061	0.007	0.078
closestToZero	0.006	0.001	0.008
compareHits	0.116	0.007	0.130
compareReplicaPlates	0.037	0.004	0.043
compareReplicateSD	0.333	0.015	0.363
compareReplicateSDPerScreen	0.523	0.022	0.562
compareReplicates	0.289	0.015	0.315
controlDensity	0.087	0.008	0.105
controlDensityPerPlate	0.323	0.021	0.348
controlDensityPerScreen	0.151	0.012	0.167
controlNorm	0.033	0.003	0.040
createSubset	0.007	0.002	0.008
discardLabtek	0.008	0.002	0.009
discardWells	0.010	0.001	0.011
divNorm	0.027	0.003	0.030
divideChannels	0.006	0.001	0.008
eraseDataSetColumn	0.021	0.001	0.023
findReplicates	0.011	0.003	0.013
furthestFromZero	0.006	0.001	0.007
generateDatasetFile	0.020	0.001	0.025
generateRepMatNoFilter	0.013	0.002	0.015
generateReplicateMat	0.023	0.002	0.025