[BioC] Annotate package not working
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Jan 9 23:13:21 CET 2014
----- 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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