[BioC] problem with AnnotationDbi

[Mark Kimpel]

The code below, which produces the error message and sessionInfo which
follow, was working last week but now is not. I got into this because
I am having trouble with the Category package and wanted to rebuild my
build of ragene10stv1.db package that Category was depending on. This
build, which had gone uneventfully last week, produced the error
below. I moved both the rat.db0 and ragene10stv1.db packages outside
of my site-library directory and reinstalled rat.db using biocLite,
thinking that perhaps I wasn't supposed to be installing an
AnnotationDbi package on top of an identical one. This didn't help so
I provide below a truncated, example, which does require prior
installation of AnnotationDbi and rat.db0.

Mark

test.vec <- c(10701630,10701632,10701636,10701643,10701648,10701654,10701663,10701666,10701668,10701671,10701674,10701679,10701684,10701689,10701691,10701697,10701699,10701709,10701714,10701717,NA,NA,292438,502213,679691,308257,292449,NA,678740,678740,679691,292450,679825,NA,NA,NA,292462,308265,NA,292464)
output.mat <- matrix(test.vec, ncol = 2)
write.table(output.mat, "RaGene-1_0-st-v1.eg.csv", col.names = FALSE,
row.names = FALSE, sep = "\t")

require(AnnotationDbi)

makeRATCHIP_DB(affy = FALSE,
               prefix = "ragene10stv1",
               fileName = "RaGene-1_0-st-v1.eg.csv",
               otherSrc = character(0),
               chipMapSrc =
system.file("extdata","chipmapsrc_rat.sqlite", package = "rat.db0"),
               chipSrc = system.file("extdata","chipsrc_rat.sqlite",
package = "rat.db0"),
               baseMapType = "eg",
               outputDir = .libPaths()[1],
               version = "1.0.0",
               manufacturer = "Affymetrix",
               chipName = "ragene10stv1",
               manufacturerUrl = "http://www.affymetrix.com",
               author = "Mark Kimpel",
               maintainer = "Mark Kimpel <mkimpel at iupui.edu>")
#

> makeRATCHIP_DB(affy = FALSE,
+                prefix = "ragene10stv1",
+                fileName = "RaGene-1_0-st-v1.eg.csv",
+                otherSrc = character(0),
+                chipMapSrc =
system.file("extdata","chipmapsrc_rat.sqlite", package = "rat.db0"),
+                chipSrc = system.file("extdata","chipsrc_rat.sqlite",
package = "rat.db0"),
+                baseMapType = "eg",
+                outputDir = .libPaths()[1],
+                version = "1.0.0",
+                manufacturer = "Affymetrix",
+                chipName = "ragene10stv1",
+                manufacturerUrl = "http://www.affymetrix.com",
+                author = "Mark Kimpel",
+                maintainer = "Mark Kimpel <mkimpel at iupui.edu>")
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: table metadata already exists)

Enter a frame number, or 0 to exit

1: makeRATCHIP_DB(affy = FALSE, prefix = "ragene10stv1", fileName = "RaGene-1_
2: popRATCHIPDB(affy = affy, prefix = prefix, fileName = fileName, chipMapSrc
3: getMapForOtherChipPkg(filePath = fileName, pkgName = prefix, chipMapSrc = c
4: probe2gene(baseMap = baseMap, baseMapType = baseMapType, otherSrc = otherSr
5: sqliteQuickSQL(db, "CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, va
6: sqliteExecStatement(con, statement, bind.data)

Selection: c
Enter an item from the menu, or 0 to exit
Selection: 0
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] RSQLite_0.7-0       DBI_0.2-4           AnnotationDbi_1.4.0
[4] affy_1.20.0         Biobase_2.2.0       graph_1.20.0

loaded via a namespace (and not attached):
[1] affyio_1.10.0        cluster_1.11.11      preprocessCore_1.4.0
>
------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do."
-- B. F. Skinner