ubuntu, 64bit, 14.04 LTS, R 3.2.0

log.txt

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ath1121501.db_3.1.2  org.At.tair.db_3.1.2 GOstats_2.34.0      
 [4] graph_1.46.0         Category_2.34.2      GO.db_3.1.2         
 [7] RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.30.1
[10] GenomeInfoDb_1.4.0   IRanges_2.2.3        S4Vectors_0.6.0     
[13] Matrix_1.2-0         Biobase_2.28.0       BiocGenerics_0.14.0 
[16] BiocInstaller_1.18.2

loaded via a namespace (and not attached):
 [1] splines_3.2.0          xtable_1.7-4           lattice_0.20-31       
 [4] tools_3.2.0            grid_3.2.0             AnnotationForge_1.10.1
 [7] genefilter_1.50.0      survival_2.38-1        RBGL_1.44.0           
[10] GSEABase_1.30.2        XML_3.98-1.2           annotate_1.46.0       
> library(GOstats)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: Matrix

Attaching package: ‘Matrix’

The following objects are masked from ‘package:base’:

    crossprod, tcrossprod

Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:Matrix’:

    expand

Loading required package: GO.db
Loading required package: DBI

Loading required package: graph

Attaching package: ‘GOstats’

The following object is masked from ‘package:AnnotationDbi’:

    makeGOGraph

> library(GO.db)

> library(ath1121501.db)
Loading required package: org.At.tair.db


> ls("package:ath1121501.db")
 [1] "ath1121501"             "ath1121501ACCNUM"       "ath1121501ARACYC"      
 [4] "ath1121501ARACYCENZYME" "ath1121501CHR"          "ath1121501CHRLENGTHS"  
 [7] "ath1121501CHRLOC"       "ath1121501CHRLOCEND"    "ath1121501.db"         
[10] "ath1121501_dbconn"      "ath1121501_dbfile"      "ath1121501_dbInfo"     
[13] "ath1121501_dbschema"    "ath1121501ENZYME"       "ath1121501ENZYME2PROBE"
[16] "ath1121501GENENAME"     "ath1121501GO"           "ath1121501GO2ALLPROBES"
[19] "ath1121501GO2PROBE"     "ath1121501MAPCOUNTS"    "ath1121501ORGANISM"    
[22] "ath1121501ORGPKG"       "ath1121501PATH"         "ath1121501PATH2PROBE"  
[25] "ath1121501PMID"         "ath1121501PMID2PROBE"   "ath1121501SYMBOL"      
> ?ath1121501ACCNUM
> x <- ath1121501ACCNUM
> mapped.probes <- mappedkeys(x)
> length(mapped.probes)
[1] 0