[BioC] AnnotationForge example does not work
Nicos Angelopoulos [guest]
guest at bioconductor.org
Tue Nov 27 21:22:42 CET 2012
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)
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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
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