Dear all, I am trying to reproduce the example from http://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationFo rge/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 ??????????????;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.

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/Annotation Forge/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 > > > > ??????????????;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. > > _______________________________________________ > 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 >