[BioC] Annotate package not working

Thu Jan 9 21:28:01 CET 2014

Here is a transcript where I start an R session, source my bug 
reproducing script, and then run sessionInfo():

$ R --vanilla

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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Platform: x86_64-unknown-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > source("annotation-bug.R")
Loading required package: AnnotationDbi
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,
     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

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

Error in as.list.default(envir) :
   no method for coercing this S4 class to a vector
In addition: Warning message:
In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
   No generic function found corresponding to requested imported methods 
for "as.list" from package "AnnotationDbi" (malformed exports?)
 > sessionInfo()
R version 3.0.2 (2013-09-25)
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] annotate_1.40.0      org.Hs.eg.db_2.10.1  RSQLite_0.11.4
[4] DBI_0.2-7            AnnotationDbi_1.24.0 Biobase_2.22.0
[7] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] colorspace_1.2-4 IRanges_1.20.6   stats4_3.0.2 XML_3.98-1.1
[5] xtable_1.7-2

On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote:
>
> Hi Ryan,
>
> I can't reproduce your error:
>
>>
>> library(annotate)
>> entrez.ids <- as.character(1:10)
>> lookUp(entrez.ids,
>
> + data="org.Hs.eg",
> + what="SYMBOL")
> $`1`
> [1] "A1BG"
>
> $`2`
> [1] "A2M"
>
> $`3`
> [1] "A2MP1"
>
> $`4`
> [1] NA
>
> $`5`
> [1] NA
>
> $`6`
> [1] NA
>
> $`7`
> [1] NA
>
> $`8`
> [1] NA
>
> $`9`
> [1] "NAT1"
>
> $`10`
> [1] "NAT2"
>
>>
>> sessionInfo()
>
> R version 3.0.2 (2013-09-25)
> 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] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4
> [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0
> [7] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1
>
> You might have some package higher in your search path that re-defines
> mget() somehow.
>
> Anyway, you might consider switching to select(), as it is much more
> powerful/useful than lookUp():
>
>>
>> select(org.Hs.eg.db, entrez.ids, "SYMBOL")
>
> ENTREZID SYMBOL
> 1 1 A1BG
> 2 2 A2M
> 3 3 A2MP1
> 4 4 <NA>
> 5 5 <NA>
> 6 6 <NA>
> 7 7 <NA>
> 8 8 <NA>
> 9 9 NAT1
> 10 10 NAT2
>
> Best,
>
> Jim
>
>
>
>
> On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote:
>>
>> Hi all,
>>
>> I'm having some trouble using the "lookUp" function in the "annotate"
>> package. Every time I try to call it, I get the following error:
>>
>> Error in as.list.default(envir) :
>> no method for coercing this S4 class to a vector
>>
>> I can generate this error with the following short test case:
>>
>> library(org.Hs.eg.db)
>> library(annotate)
>> entrez.ids <- as.character(1:10)
>> lookUp(entrez.ids,
>> data="org.Hs.eg",
>> what="SYMBOL")
>>
>> Alternatively, simply running the example from the lookUp help page
>> also produces the error.
>>
>> Can anyone help me get this working again?
>>
>> -Ryan Thompson
>>
>> _______________________________________________
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>> Search the archives:
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>
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099