[BioC] Annotate package not working
Ryan C. Thompson
rct at thompsonclan.org
Fri Jan 10 00:08:48 CET 2014
I've gotten this error before, and I just now randomly fixed it by
reinstalling the AnnotationDbi package over and over until I saw the
following line in the output:
Creating a generic function for ‘as.list’ from package ‘base’ in
package ‘AnnotationDbi’
I previously did not see this message while installing AnnotationDbi.
Afterwards, my example worked fine. I have no explanation for why this
keeps happening.
-Ryan
On Thu 09 Jan 2014 02:13:21 PM PST, Dan Tenenbaum wrote:
>
>
> ----- Original Message -----
>> From: "Ryan C. Thompson" <rct at thompsonclan.org>
>> To: "James W. MacDonald" <jmacdon at uw.edu>
>> Cc: "bioconductor" <bioconductor at r-project.org>
>> Sent: Thursday, January 9, 2014 12:28:01 PM
>> Subject: Re: [BioC] Annotate package not working
>>
>> 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"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> 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
>>
>
> Hmm...it works for me with the following sessionInfo, it seems the only differences are R version (I'm running R-patched) and version of xtable, but I tried a newer one and it still worked. Also, I don't have colorspace loaded.
>
> Dan
>
> R version 3.0.2 Patched (2013-12-18 r64488)
> 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] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1
>
>
>
>>
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>
>> _______________________________________________
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