Entering edit mode
Mark Cowley
▴
910
@mark-cowley-2951
Last seen 10.3 years ago
Dear list,
I just ran through the 'Creating an annotation package with a new
database schema' vignette within AnnotationDbi, verbatim, and hit an
error in 'code chunk 22', where calling:
> makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE),
nrow = nr, :
negative extents to matrix
The code's pretty complicated, so I was hoping one of the maintainers
could take a look.
method:
copy & paste each code block within: http://www.bioconductor.org/packa
ges/2.10/bioc/vignettes/AnnotationDbi/inst/doc/NewSchema.R
including the commented out code blocks re downloading targetscan and
populating the database:
...
###################################################
### code chunk number 22: build new package (eval = FALSE)
###################################################
> seed <- new("AnnDbPkgSeed",
Package = package,
Version = "5.0-1",
PkgTemplate = packagedir,
AnnObjPrefix = "targetscan.Hs.eg",
Title = "TargetScan miRNA target predictions for human",
Author = "Gabor Csardi <gabor.csardi@foo.bar>",
Maintainer = "Gabor Csardi <gabor.csardi@foo.bar>",
organism = "Homo sapiens",
species = "Human",
biocViews = "AnnotationData, FunctionalAnnotation",
DBschema = "TARGETSCAN_DB",
AnnObjTarget = "TargetScan (Human)",
manufacturer = "None",
manufacturerUrl = "None"
)
> unlink(paste(tempdir(), sep=.Platform$file.sep, package),
recursive=TRUE)
> makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
# Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE),
nrow = nr, :
# negative extents to matrix
> traceback()
# 4: matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow
= nr,
# dimnames = list(rn, cn))
# 3: Ops.data.frame(type, "ChipDb")
# 2: makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
# 1: makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
> options(error=recover)
> makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
# Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE),
nrow = nr, :
# negative extents to matrix
#
# Enter a frame number, or 0 to exit
#
# 1: makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
# 2: makeAnnDbPkg(seed, dbfile, dest_dir = tempdir())
# 3: Ops.data.frame(type, "ChipDb")
# 4: matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow
= nr, dimn
#
# Selection: 3
# Called from: Ops.data.frame(type, "ChipDb")
# Browse[1]> value
# [[1]]
# logical(0)
I did this twice, from scratch, with the same result, in both R
2.15.0, and R 2.15.1
Could you please also make these 2 changes to the vignette as well:
1) code chunk 18, final block has a tab character hiding in this line:
"INSERT INTO targets\tVALUES(:miR_Family,"
2) code chunk 15: zip.file.extract is defunct as of R 2.15.1 (but was
fine in R 2.15.0). I've updated this code block:
targetfile <- file.path(tempdir(), "Predicted_Targets_Info.txt")
targetfile.zip <- paste(targetfile, sep="", ".zip")
if (!file.exists(targetfile)) {
if (!file.exists(targetfile.zip)) {
data.url <- paste(sep="",
"http://www.targetscan.org/vert_50/",
"vert_50_data_download/Predicted_Targets_Info.txt.zip")
download.file(data.url, destfile=targetfile.zip)
}
unzip( targetfile.zip, basename(targetfile), exdir=tempdir() )
file.exists(targetfile) || warning("Didn't extract targetfile
from zip")
}
familyfile <- file.path(tempdir(), "miR_Family_Info.txt")
familyfile.zip <- paste(familyfile, sep="", ".zip")
if (!file.exists(familyfile)) {
if (!file.exists(familyfile.zip)) {
data.url <- paste(sep="",
"http://www.targetscan.org/vert_50/",
"vert_50_data_download/miR_Family_Info.txt.zip")
download.file(data.url, destfile=familyfile.zip)
}
unzip( familyfile.zip, basename(familyfile), exdir=tempdir() )
file.exists(familyfile) || warning("Didn't extract familyfile
from zip")
}
taxfile <- file.path(getwd(), "names.dmp")
taxfile.zip <- file.path(tempdir(), "taxdmp.zip")
if (!file.exists(taxfile)) {
if (!file.exists(taxfile.zip)) {
data.url <-
"ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip"
download.file(data.url, destfile=taxfile.zip)
}
unzip( taxfile.zip, "names.dmp", exdir=tempdir() )
file.exists(taxfile) || warning("Didn't extract taxfile from
zip")
}
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.1
[4] Biobase_2.16.0 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] IRanges_1.14.4 stats4_2.15.1 tools_2.15.1
cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------
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