hi; I am trying to use 'getNearestTranscript' and 'getNesrestTSS' for annotation of 450K DNA-me array data as in the ref. manual, but I get:

> ?getNearestTranscript
No documentation for âgetNearestTranscriptâ in specified packages and libraries:
you could try â??getNearestTranscriptâ> 

?getNesrestTSS

No documentation for âgetNesrestTSSâ in specified packages and libraries:
you could try â??getNesrestTSSâ

What am I doing wrong? 

Thanks

Hamid Bolouri (great new support web site, btw!)

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] FDb.InfiniumMethylation.hg19_2.0.10   BSgenome.Hsapiens.UCSC.hg19_1.3.1000
 [3] BSgenome_1.32.0                       Biostrings_2.32.1
 [5] XVector_0.4.0                         GenomicFeatures_1.16.3
 [7] GenomicRanges_1.16.4                  IRanges_1.22.10
 [9] IlluminaHumanMethylation450k.db_2.0.7 org.Hs.eg.db_2.14.0
[11] RSQLite_0.11.4                        DBI_0.3.1
[13] AnnotationDbi_1.26.1                  GenomeInfoDb_1.0.2
[15] Biobase_2.24.0                        BiocGenerics_0.10.0
[17] BiocInstaller_1.14.3

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.4           BBmisc_1.7
 [4] BiocParallel_0.6.1      biomaRt_2.20.0          bitops_1.0-6
 [7] brew_1.0-6              checkmate_1.5.0         codetools_0.2-9
[10] digest_0.6.4            fail_1.2                foreach_1.4.2
[13] GenomicAlignments_1.0.6 iterators_1.0.7         RCurl_1.95-4.3
[16] Rsamtools_1.16.1        rtracklayer_1.24.2      sendmailR_1.2-1
[19] stats4_3.1.1            stringr_0.6.2           tools_3.1.1
[22] XML_3.98-1.1            zlibbioc_1.10.0

EDIT:

You seem to have an older version of BioC. I would start with

library(BiocInstaller)
biocLite("BiocUpgrade")

I have, after loading the FDb package:

> ls(2)
 [1] "FDb.InfiniumMethylation.hg19" "get27k"                      
 [3] "get450k"                      "getNearest"                  
 [5] "getNearestGene"               "getNearestTranscript"        
 [7] "getNearestTSS"                "getPlatform"                 
 [9] "hm27ToHg19"                   "lift27kToHg19"  

And

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] FDb.InfiniumMethylation.hg19_2.1.999   
 [2] org.Hs.eg.db_3.0.0                     
 [3] RSQLite_1.0.0                          
 [4] DBI_0.3.1                              
 [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
 [6] GenomicFeatures_1.18.2                 
 [7] AnnotationDbi_1.28.1                   
 [8] Biobase_2.26.0                         
 [9] GenomicRanges_1.18.1                   
[10] GenomeInfoDb_1.2.2                     
[11] IRanges_2.0.0                          
[12] S4Vectors_0.4.0                        
[13] BiocGenerics_0.12.0                    

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.8             
 [4] BiocParallel_1.0.0      biomaRt_2.22.0          Biostrings_2.34.0      
 [7] bitops_1.0-6            brew_1.0-6              checkmate_1.5.0        
[10] codetools_0.2-9         digest_0.6.4            fail_1.2               
[13] foreach_1.4.2           GenomicAlignments_1.2.0 iterators_1.0.7        
[16] RCurl_1.95-4.3          Rsamtools_1.18.1        rtracklayer_1.26.1     
[19] sendmailR_1.2-1         stringr_0.6.2           tools_3.1.1            
[22] XML_3.98-1.1            XVector_0.6.0           zlibbioc_1.12.0 

That did it! 

Thanks for the super-quick response.

Hamid