[BioC] AnnBuilder error: parseData can't access some tmp file

Benjamin Otto b.otto at uke.uni-hamburg.de
Fri Dec 22 14:34:47 CET 2006

Dear bioconductors,

The parseData function of AnnBuilder terminates with a strange behaviour on
my machine. When I follow the AnnBuilder.pdf instructions parseData
contstructs some temporary file in a tmp folder and fails afterwards in
accessing another one (the same one?). Interesting is, that the name of the
file created and the name of one it tries to open is different.

The following command:

> llMapping <- parseData(eg, eg at accession)

returns this error message:

Fehler in file(file, "r") : kann Verbindung nicht öffnen
Zusätzlich: Warning message:
kann Datei 'y:/tmp/RtmpKfS7qb/tempOut63af6892' nicht öffnen. Grund 'No such
file or directory' 

The name of the file created during the process is "file26573e03Tll_tmpl"
and "tempOut63af6892" does definitly not exist. Below you will find the
complete code I used and the sessionInfo.


R version 2.4.0 (2006-10-03) 

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

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

other attached packages:
   biomaRt      RCurl AnnBuilder    RSQLite        DBI   annotate        XML
   "1.8.1"    "0.8-0"   "1.12.0"   "0.4-15"   "0.1-12"   "1.12.1"    "1.4-0"


pkgpath <- .find.package("AnnBuilder")
docFiles <- file.path(pkgpath, c("TITLE", "DESCRIPTION", "INDEX"))
headers <- c("", "Description:\n\n", "Index:\n\n")
footers <- c("\n", "\n", "")
for (i in which(file.exists(docFiles))) {
writeLines(headers[i], sep = "")
writeLines(readLines(docFiles[i]) )
writeLines(footers[i], sep = "")

geneNMap <- matrix(c("32468_f_at", "D90278;M16652", "32469_at", "L00693",
"32481_at", "AL031663", "33825_at", "X68733",
"35730_at", "X03350", "36512_at", "L32179",
"38912_at", "D90042", "38936_at", "M16652",
"39368_at", "AL031668"), ncol = 2, byrow = TRUE)
write.table(geneNMap, file = "geneNMap", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)

srcObjs <- list()
egUrl <-
ugUrl <-
eg <- EG(srcUrl = egUrl, parser = file.path(pkgpath, "scripts",
"gbLLParser"), baseFile = "geneNMap", accession = "Tll_tmpl.gz",
built = "N/A", fromWeb = TRUE)
ug <- UG(srcUrl = ugUrl, parser = file.path(pkgpath,
"scripts", "gbUGParser"), baseFile = "geneNMap",
organism = "Homo sapiens", built = "N/A", fromWeb = TRUE)
srcObjs[["eg"]] <- eg
srcObjs[["ug"]] <- ug

llMapping <- parseData(eg, eg at accession)

Benjamin Otto
Universitaetsklinikum Eppendorf Hamburg
Institut fuer Klinische Chemie
Martinistrasse 52
20246 Hamburg

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