Question: AnnotationForge example does not work
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6.8 years ago by
Guest User12k
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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.
go cancer chipname probe affy • 790 views
ADD COMMENTlink modified 6.8 years ago by James F. Reid120 • written 6.8 years ago by Guest User12k
Answer: AnnotationForge example does not work
0
gravatar for James F. Reid
6.8 years ago by
James F. Reid120
James F. Reid120 wrote:
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 >
ADD COMMENTlink written 6.8 years ago by James F. Reid120
Hi James, Thanks for this. I can confirm the call to makeDBPackage() completes once 'org.Hs.eg.db' has been installed and loaded. SQLForge.R itself then fails on file.rename(file.path(tmpout, "hcg110.db"),file.path(tmpout, "foo.db")) but this is just as a matter of general info. In my run there was no such file in the tmpout directory. The package built correctly and I was able to load it. Hope the dependency to 'org.Hs.eg.db' becomes explicit both in the SQLForge.pdf and the sources. Many thanks also to the developers and maintainers of these packages. Regards, Nicos Angelopoulos --- http://bioinformatics.nki.nl/~nicos/ On Wed, 28 Nov 2012 13:55:39 +0000 "James F. Reid" <reidjf at="" gmail.com=""> wrote: > 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. > >
ADD REPLYlink written 6.8 years ago by Nicos Angelopoulos NKI Amsterdam10
Thanks for finding this problem! It shall be fixed. Marc On 11/28/2012 07:38 AM, Nicos Angelopoulos (NKI Amsterdam) wrote: > Hi James, > > Thanks for this. > > I can confirm the call to makeDBPackage() > completes once 'org.Hs.eg.db' has been installed and loaded. > > SQLForge.R itself then fails on > file.rename(file.path(tmpout, "hcg110.db"),file.path(tmpout, "foo.db")) > but this is just as a matter of general info. > In my run there was no such file in the tmpout directory. > The package built correctly and I was able to load it. > > Hope the dependency to 'org.Hs.eg.db' becomes explicit both in the > SQLForge.pdf and the sources. > > Many thanks also to the developers and maintainers of these packages. > > Regards, > > Nicos Angelopoulos > --- > http://bioinformatics.nki.nl/~nicos/ > > On Wed, 28 Nov 2012 13:55:39 +0000 > "James F. Reid"<reidjf at="" gmail.com=""> wrote: > >> 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. >> >>
ADD REPLYlink written 6.8 years ago by Marc Carlson7.2k
I should probably say a little bit more than this. The issue was caused by a change that was made after this vignette was originally written. An appropriate org package is really required to check (or use) any associated chip package that gets made. So when the package is almost done, the software is trying to connect to an org package to make sure that the keys are present and working etc. (and then failing to find one). The vignette should really reflect this requirement, and so I will now change it. Marc On 11/28/2012 11:11 AM, Marc Carlson wrote: > Thanks for finding this problem! It shall be fixed. > > Marc > > > On 11/28/2012 07:38 AM, Nicos Angelopoulos (NKI Amsterdam) wrote: >> Hi James, >> >> Thanks for this. >> >> I can confirm the call to makeDBPackage() >> completes once 'org.Hs.eg.db' has been installed and loaded. >> >> SQLForge.R itself then fails on >> file.rename(file.path(tmpout, "hcg110.db"),file.path(tmpout, "foo.db")) >> but this is just as a matter of general info. >> In my run there was no such file in the tmpout directory. >> The package built correctly and I was able to load it. >> >> Hope the dependency to 'org.Hs.eg.db' becomes explicit both in the >> SQLForge.pdf and the sources. >> >> Many thanks also to the developers and maintainers of these packages. >> >> Regards, >> >> Nicos Angelopoulos >> --- >> http://bioinformatics.nki.nl/~nicos/ >> >> On Wed, 28 Nov 2012 13:55:39 +0000 >> "James F. Reid"<reidjf at="" gmail.com=""> wrote: >> >>> 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. >>> >>> > > _______________________________________________ > 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
ADD REPLYlink written 6.8 years ago by Marc Carlson7.2k
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