[BioC] GO terms: Annotation for HumanMethylation450

[Marc Carlson]

Wow.  That is some old software you have there.  You should really 
update pronto.  At the very least, you probably need a newer version of 
R, AnnotationDbi, and GO.db.

Whenever you see strange things happening, you should probably start by 
updating to the latest version of your software. Bioconductor has a very 
active development community, and so a year is actually a very long time 
to go without updates.

Here is my sessionInfo() (this is my older version for R from the the 
older release last fall).  And I note that even what I list here could 
be a bit more up to date than it presently is.

R version 2.15.2 Patched (2012-11-04 r61084)
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=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GO.db_2.8.0          RSQLite_0.11.2       DBI_0.2-5
[4] AnnotationDbi_1.20.6 Biobase_2.18.0       BiocGenerics_0.4.0
[7] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] IRanges_1.16.4  parallel_2.15.2 stats4_2.15.2   tools_2.15.2


And later this week, there should be another release with even newer 
software...


   Marc



On 04/02/2013 03:32 PM, Jinyan Huang wrote:
>> library(GO.db)
> Loading required package: AnnotationDbi
> Loading required package: BiocGenerics
>
> Attaching package: ‘BiocGenerics’
>
> The following object(s) are masked from ‘package:stats’:
>
>      xtabs
>
> The following object(s) are masked from ‘package:base’:
>
>      anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>      get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
>      pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>      rownames, sapply, setdiff, table, tapply, union, unique
>
> Loading required package: Biobase
> Welcome to Bioconductor
>
>      Vignettes contain introductory material; view with
>      'browseVignettes()'. To cite Bioconductor, see
>      'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: DBI
>
>>   ids = c( "GO:0008150", "GO:0001869")
>> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))
> Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> 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=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GO.db_2.7.1          RSQLite_0.11.2       DBI_0.2-5
> [4] AnnotationDbi_1.18.4 Biobase_2.16.0       BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.4 stats4_2.15.1
>
> On Tue, Apr 2, 2013 at 6:28 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>> Hi Jinyan,
>>
>> I can't reproduce this problem in release or devel.
>>
>>
>> So can you please follow the posting guidelines here:
>>
>> http://www.bioconductor.org/help/mailing-list/posting-guide/
>>
>> And give me the output of your sessionInfo()?
>>
>>
>> Thanks,
>>
>>
>>    Marc
>>
>>
>>
>> On 04/02/2013 02:09 PM, Jinyan Huang wrote:
>>> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))
>>
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>
>