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tzaquin
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@tzaquin-22772
Last seen 4.9 years ago
Hi all, hope you might help me. I'm not very computer savvy, yet I try to create an org.db as it didn't look too hard. And in fact, 3 days ago I was able to do it, but then I tried to do another one and I got this error: .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name. I thought it might be because I mistakingly did not have unique column names, but I couldn't find a problem with it. Then I went back to the authors' examples:
> setwd("~/test/")
> library(AnnotationForge)
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 objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
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
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
>
> finchFile <- system.file("extdata","finch_info.txt",
+ package="AnnotationForge")
> finch <- read.table(finchFile,sep="\t")
>
> fSym <- finch[,c(2,3,9)]
> fSym <- fSym[fSym[,2]!="-",]
> fSym <- fSym[fSym[,3]!="-",]
> colnames(fSym) <- c("GID","SYMBOL","GENENAME")
>
> fChr <- finch[,c(2,7)]
> fChr <- fChr[fChr[,2]!="-",]
> colnames(fChr) <- c("GID","CHROMOSOME")
>
> finchGOFile <- system.file("extdata","GO_finch.txt",
+ package="AnnotationForge")
> fGO <- read.table(finchGOFile,sep="\t")
> fGO <- fGO[fGO[,2]!="",]
> fGO <- fGO[fGO[,3]!="",]
> colnames(fGO) <- c("GID","GO","EVIDENCE")
>
> makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO,
+ version="0.1",
+ maintainer="Some One <so@someplace.org>",
+ author="Some One <so@someplace.org>",
+ outputDir = ".",
+ tax_id="59729",
+ genus="Taeniopygia",
+ species="guttata",
+ goTable="go")
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in ./org.Tguttata.eg.db
Now deleting temporary database file
[1] "./org.Tguttata.eg.db"
There were 50 or more warnings (use warnings() to see the first 50)
> install.packages("./org.Tguttata.eg.db", repos=NULL, type="source")
* installing *source* package 'org.Tguttata.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'org.Tguttata.eg.db'
finding HTML links ... done
org.Tguttata.egBASE html
org.Tguttata.egORGANISM html
org.Tguttata.eg_dbconn html
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (org.Tguttata.eg.db)
> library(org.Tguttata.eg.db)
> keytypes(org.Tguttata.eg.db)
[1] "CHROMOSOME" "EVIDENCE" "EVIDENCEALL" "GENENAME" "GID" "GO" "GOALL" "ONTOLOGY"
[9] "ONTOLOGYALL" "SYMBOL"
> keys(org.Tguttata.eg.db,"GO")
Error in .deriveTableNameFromField(field = keytype, x) :
Two fields in the source DB have the same name.
if anyone can help, I will ver much appreciate it.
Tal
forgot to add the trace back
So, I'm guessing there is some kind of duplication? but then, why is that?
Tal