AnnBuilder error: parseData can't access some tmp file
1
0
Entering edit mode
Benjamin Otto ▴ 830
@benjamin-otto-1519
Last seen 8.1 years ago
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 ?ffnen Zus?tzlich: Warning message: kann Datei 'y:/tmp/RtmpKfS7qb/tempOut63af6892' nicht ?ffnen. 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. Regards, Benjamin SessionInfo: ---------------------------------------------------------------------- ------ ---- R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [8] "base" other attached packages: biomaRt RCurl AnnBuilder RSQLite DBI annotate XML Biobase "1.8.1" "0.8-0" "1.12.0" "0.4-15" "0.1-12" "1.12.1" "1.4-0" "1.12.2" CODE: ---------------------------------------------------------------------- ------ ---- library(AnnBuilder) 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) makeSrcInfo() srcObjs <- list() egUrl <- "http://www.bioconductor.org/datafiles/wwwsources" ugUrl <- "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz" 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
AnnBuilder PROcess biomaRt AnnBuilder PROcess biomaRt • 512 views
ADD COMMENT
0
Entering edit mode
Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Benjamin, It seems that you are trying execute the example code in AnnBuilder vigentte without any modifications. There is a line right after the example: "the urls used in the example are for demonstration purpose only." There is no such file: http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz But the unzipped version is available at the "data" folder. Maybe you could use that file and invoke parseData with "fromWeb=FALSE". You probably don't need to interface with "parseData" unless you want to build VERY customized annotation packages. There are several existing builder functions such as ABPkgBuilder, GOPkgBuilder, etc. They can be used to build annotation packages via a single function call. If you have to create customized builder functions, please (if you don't mind) illustrate more on your task next time. Many thanks. HTH nianhua Nianhua Li Computational Biology, PHS, FHCRC
ADD COMMENT

Login before adding your answer.

Traffic: 401 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6