[BioC] AnnotationForge example does not work
James F. Reid
reidjf at gmail.com
Wed Nov 28 14:55:39 CET 2012
Hi Nicos,
I think installing 'org.Hs.eg.db' will solve the problem. It is a
required package when you load your newly created custom annotation package.
HTH
J.
On 27/11/12 20:22, Nicos Angelopoulos [guest] wrote:
>
>
> Dear all,
>
> I am trying to reproduce the example from
>
> http://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationForge/inst/doc/SQLForge.pdf
>
> but i get an
>
> " subscript out of bounds"
>
> error.
>
> Please see included transcript.
>
> Also note that in the latest version of the vignettes
> (23rd Nov 2012) the R command
> tmpout = tempdir()
> is missing.
>
> Many thanks,
>
> Nicos Angelopoulos
> ---
> http://bioinformatics.nki.nl/~nicos
>
>
>
> άμπελος;okt12/nicos% R --vanilla
>
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> 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.
>
>> library(AnnotationForge)
> 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: AnnotationDbi
>> read.table(system.file("extdata", "hcg110_ID",
> + package="AnnotationDbi"),
> + sep = "\t", header = FALSE, as.is = TRUE)[1:5,]
> V1 V2
> 1 1000_at X60188
> 2 1001_at X60957
> 3 1002_f_at X65962
> 4 1003_s_at X68149
> 5 1004_at X68149
>> available.db0pkgs()
> [1] "anopheles.db0" "arabidopsis.db0" "bovine.db0" "canine.db0"
> [5] "chicken.db0" "chimp.db0" "ecoliK12.db0" "ecoliSakai.db0"
> [9] "fly.db0" "human.db0" "malaria.db0" "mouse.db0"
> [13] "pig.db0" "rat.db0" "rhesus.db0" "worm.db0"
> [17] "xenopus.db0" "yeast.db0" "zebrafish.db0"
>> available.dbschemas()
> [1] "ARABIDOPSISCHIP_DB" "BOVINECHIP_DB" "BOVINE_DB"
> [4] "CANINECHIP_DB" "CANINE_DB" "CHICKENCHIP_DB"
> [7] "CHICKEN_DB" "ECOLICHIP_DB" "ECOLI_DB"
> [10] "FLYCHIP_DB" "FLY_DB" "GO_DB"
> [13] "HUMANCHIP_DB" "HUMANCROSSCHIP_DB" "HUMAN_DB"
> [16] "INPARANOIDDROME_DB" "INPARANOIDHOMSA_DB" "INPARANOIDMUSMU_DB"
> [19] "INPARANOIDRATNO_DB" "INPARANOIDSACCE_DB" "KEGG_DB"
> [22] "MALARIA_DB" "MOUSECHIP_DB" "MOUSE_DB"
> [25] "PFAM_DB" "PIGCHIP_DB" "PIG_DB"
> [28] "RATCHIP_DB" "RAT_DB" "WORMCHIP_DB"
> [31] "WORM_DB" "YEASTCHIP_DB" "YEAST_DB"
> [34] "ZEBRAFISHCHIP_DB" "ZEBRAFISH_DB"
>> tmpout = tempdir()
>> hcg110_IDs = system.file("extdata",
> + "hcg110_ID",
> + package="AnnotationDbi")
>> makeDBPackage("HUMANCHIP_DB",
> + affy=FALSE,
> + prefix="hcg110",
> + fileName=hcg110_IDs,
> + baseMapType="gb",
> + outputDir = tmpout,
> + version="1.0.0",
> + manufacturer = "Affymetrix",
> + chipName = "Human Cancer G110 Array",
> + manufacturerUrl = "http://www.affymetrix.com")
> Loading required package: RSQLite
> Loading required package: DBI
> baseMapType is gb or gbNRef
> Prepending Metadata
> Creating Genes table
> Appending Probes
> Found 2059 Probe Accessions
> Appending Gene Info
> Found 1436 Gene Names
> Found 1436 Gene Symbols
> Appending Chromosomes
> Appending Cytogenetic Locations
> Appending Omim
> Appending RefSeq
> Appending Pubmed
> Appending Unigene
> Appending ChrLengths
> Appending 3 GO tables
> Appending 3 GO ALL tables
> Appending KEGG
> Appending EC
> Appending Chromosome Locations
> Appending Pfam
> Appending Prosite
> Appending Alias
> Appending Ensembl
> Appending Uniprot
> Appending Metadata
>
>
> simplifying probes table
> dropping redundant data
> Error in .makeAnnDbPkg(x, dbfile, dest_dir = ".", no.man = FALSE, ...) :
> subscript out of bounds
>
>
>> traceback()
> 5: .makeAnnDbPkg(x, dbfile, dest_dir = ".", no.man = FALSE, ...)
> 4: makeAnnDbPkg(seed, file.path(outputDir, paste0(prefix, ".sqlite")),
> dest_dir = outputDir)
> 3: makeAnnDbPkg(seed, file.path(outputDir, paste0(prefix, ".sqlite")),
> dest_dir = outputDir)
> 2: AnnotationForge:::.makeHUMANCHIP_DB(...)
> 1: makeDBPackage("HUMANCHIP_DB", affy = FALSE, prefix = "hcg110",
> fileName = hcg110_IDs, baseMapType = "gb", outputDir = tmpout,
> version = "1.0.0", manufacturer = "Affymetrix", chipName = "Human Cancer G110 Array",
> manufacturerUrl = "http://www.affymetrix.com")
>>
>
>
> -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] RSQLite_0.11.2 DBI_0.2-5 AnnotationForge_1.0.2
> [4] AnnotationDbi_1.20.3 Biobase_2.18.0 BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.4 parallel_2.15.2 stats4_2.15.2 tools_2.15.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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