[BioC] Re : bug with AnnBuilder and parser

[Nianhua Li]

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/llParser") :
>         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