RNAither 2.1.1
Nora Rieber
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither | | Last Changed Rev: 56555 / Revision: 56603 | | Last Changed Date: 2011-07-05 07:47:19 -0700 (Tue, 05 Jul 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.1.1'
* 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 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 ... NOTE
Note: significantly better compression could be obtained
by using tools::resaveRdaFiles() or R CMD build --resave-data
old_size new_size compress
datasetDrosophila.rda 763Kb 506Kb xz
* 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 1.3-01)
** 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 1.3-01)
* DONE (RNAither)