[BioC] Annotate package not working
Martin Morgan
mtmorgan at fhcrc.org
Fri Jan 10 04:15:47 CET 2014
On 01/09/2014 03:08 PM, Ryan C. Thompson wrote:
> 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.
Hopefully this isn't random, but some other uncontrolled variable.
I can reproduce (something like) this by installing AnnotationDbi when there is
a generic 'as.list' available in the global environment at install time, e.g., I
added this line to my .Rprofile
setGeneric("as.list")
Then I installed AnnotationDbi
R -e "source('http://bioconductor.org/biocLite.R'); biocLite('AnnotationDbi')"
(maybe you load a package or something similar during an interactive session
where you subsequently installed AnnotationDbi?). Then when I run Ryan's
commands in a new R session
R -f annotation-bug.R
I get
> library(annotate)
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?)
> entrez.ids <- as.character(1:10)
> lookUp(entrez.ids, data="org.Hs.eg", what="SYMBOL")
Error in as.list.default(envir) :
no method for coercing this S4 class to a vector
Calls: lookUp -> mget -> mget -> as.list -> as.list.default
Execution halted
(I only see the warning the first time I load annotate...) Maybe there's a
variation of this where there's a generic available at install time but a
different generic at run time, e.g., from one package masking another?
I think the work-around is to install packages in a new session started with
R --vanilla
and a solution is to create a generic as.list in BiocGenerics (AnnotationDbi
will see and import this).
Martin
>
> -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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>
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