Question: Re : bug with AnnBuilder and parser
0
gravatar for Nianhua Li
12.3 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Hi, gregory, I also cc the list since it will benefit others. You'd better update your R and AnnBuilder. R 2.5 has just released last month. After installing R, please use "biocLite()" to get the latest AnnBuilder (1.14.0 for R 2.5 and 1.15.2 for R 2.6) and try from there. Your file permissions for the parsers are fine. hope it helps nianhua gregory voisin wrote: > Hi Nianhua > > 1. > Could you try invoking ABPkgBuilder directly? the same error message > > ABPkgBuilder(baseName= mybase, srcUrls= mySrcUrls, baseMapType = > mybasetype, pkgName = "monPackageAnnoted", pkgPath = mydir, organism = > "Homo sapiens", version = "1.0", author = list (authors = "Greg_Voisin, > Amelie Ouellet", maintainer = "voisingreg at yahoo.fr > <mailto:voisingreg at="" yahoo.fr="">"), fromWeb =TRUE) > Warning: use of NULL environment is deprecated > Error in "parser<-"(`*tmp*`, value = > "/soft/bioinfo/linux/R-2.3.1/lib/R/library/AnnBuilder/scripts/llPars er") : > no direct or inherited method for function 'parser<-' for this call > > 2. >> sessionInfo() > Version 2.3.1 (2006-06-01) > i686-pc-linux-gnu > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > other attached packages: > AnnBuilder annotate XML Biobase > "1.4.21" "1.10.0" "1.6-3" "1.10.1" > > 3. remarks: I have only right of read for script/llParser: > drwxr-xr-x 2 adsoft users 4096 Apr 13 10:12 . > drwxr-xr-x 14 adsoft users 4096 Apr 13 10:12 .. > -rw-r--r-- 1 adsoft users 12912 Apr 13 10:12 ABPkgsBuilder.R > -rw-r--r-- 1 adsoft users 828 Apr 13 10:12 dataPkgLoad.R > -rw-r--r-- 1 adsoft users 3782 Apr 13 10:12 dbLLParser > -rw-r--r-- 1 adsoft users 852 Apr 13 10:12 gb2LLUGParser > -rw-r--r-- 1 adsoft users 795 Apr 13 10:12 gbLLParser > -rw-r--r-- 1 adsoft users 1260 Apr 13 10:12 gbNRef2LLParser > -rw-r--r-- 1 adsoft users 1007 Apr 13 10:12 gbUGParser > -rw-r--r-- 1 adsoft users 2334 Apr 13 10:12 geneLocClass.R > -rw-r--r-- 1 adsoft users 2613 Apr 13 10:12 geneLoc-class.Rd > -rw-r--r-- 1 adsoft users 1396 Apr 13 10:12 GO2ProbeParser > -rw-r--r-- 1 adsoft users 985 Apr 13 10:12 GO2ProbeParser4LL > -rw-r--r-- 1 adsoft users 671 Apr 13 10:12 imageUGParser > -rw-r--r-- 1 adsoft users 801 Apr 13 10:12 ll2GBUGParser > -rw-r--r-- 1 adsoft users 899 Apr 13 10:12 llMappingParser > -rw-r--r-- 1 adsoft users 509 Apr 13 10:12 llNGOParser > -rw-r--r-- 1 adsoft users 5136 Apr 13 10:12 llParser > -rw-r--r-- 1 adsoft users 4636 Apr 13 10:12 llParser4LL > -rw-r--r-- 1 adsoft users 915 Apr 13 10:12 llRefSeqParser > -rw-r--r-- 1 adsoft users 2108 Apr 13 10:12 print.ABQCList.Rd > -rw-r--r-- 1 adsoft users 3827 Apr 13 10:12 SPParser > -rw-r--r-- 1 adsoft users 688 Apr 13 10:12 ugLLParser > -rw-r--r-- 1 adsoft users 758 Apr 13 10:12 ugUGParser > > > Thanks for your help > > Greg
annotate annbuilder • 384 views
ADD COMMENTlink modified 12.3 years ago • written 12.3 years ago by Nianhua Li870
Answer: Re : bug with AnnBuilder and parser
0
gravatar for Nianhua Li
12.3 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Hi Gregory, I couldn't repeat your error with your base mapping file. I am using linux though. The script I used was: library(AnnBuilder) ABPkgBuilder(baseName="probeset_gb.txt", baseMapType="gbNRef", pkgName="monPackageAnnoted", pkgPath=".", organism="Homo sapiens", version="1.0", author=list( authors="Greg_Voisin, Amelie Ouellet", maintainer="Greg_Voisin<voisingreg at="" yahoo.fr="">" ) ) But I didn't got any annotation at the beginning. It took me quite a while, and with my colleague's help, to realize that your base mapping file has "\r" at the end of each line. It caused some problems with the perl scripts being invoked by ABPkgBuilder. You shouldn't have this problem because you are using windows anyway. I have never used AnnBuilder on windows, therefore can't give you more useful advices. But I will send you the source package of "monPackageAnnoted" offline. best nianhua --------------------------------------------------------------- Hi Nianhua, I have update version of R and Annbuilder ( on windows system, I wait for the same update on my unix system):: > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=French_Canada.1252;LC_CTYPE=French_Canada.1252;LC_MONETARY= French_Canada.1252;LC_NUMERIC=C;LC_TIME=French_Canada.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.16.0" "1.14.0" "1.14.1" "1.7-1" "1.14.0" Then, I reload the same code ....but message error nd no creation of package... > library (AnnBuilder) Le chargement a n?cessit? le package : Biobase Le chargement a n?cessit? le package : tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Le chargement a n?cessit? le package : XML Le chargement a n?cessit? le package : annotate > data_gb = read.table("probeset_gb.txt" , sep = "\t", header=FALSE, as.is=TRUE) > mybase = file.path("probeset_gb.txt") > > mybasetype= "gb" > mydir = getwd() > LL_url = getSrcUrl(src = "LL", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE) > KEGG_url = getSrcUrl(src = "KEGG", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE) > UG_url = getSrcUrl(src = "UG", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE) > mySrcUrls = c(LL_url, KEGG_url, UG_url) > ABPkgBuilder(baseName= mybase, srcUrls= mySrcUrls, baseMapType = mybasetype, pkgName = "monPackageAnnoted", pkgPath = mydir, organism = "Homo sapiens", version = "1.0", author = list (authors = "Greg_Voisin, Amelie Ouellet", maintainer = "voisingreg at ...."), fromWeb =TRUE) Attachement du package : 'GO' The following object(s) are masked from package:AnnBuilder : GO Erreur dans function (classes, fdef, mtable) : unable to find an inherited method for function "baseFile<-", for signature "NULL" I join my file input ( probeset /genbankID) Can you try in your system? Thanks ,Nianhua , for your help in R problems... Greg
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