[BioC] AnnBuilder package: problem with gbNRef

[Craddock, Richard C. (CDC/NCID/VR) (CTR)]

Sorry to send the original in html.  Hopefully this works better ....

-cameron

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----

Hello all,

I am having a similar problem to Weijun's but the posted fixes are not
working for me.  I am trying to build a "gbNRef" package but the
annotation information is missing.  I have upgraded to AnnBuilder 1.11.5
from svn, and I have tried both the two and three column base file.  I
have intermittent problems connecting to the NCBI ftp site, so I copied
the necessary files locally.  Here is the code I am using:

myBase <- "/home/cameron/microarray_data/mwg40ka_basname_named.tdf"
myBaseType <- "gbNRef"
 

mySrcUrls <- getSrcUrl("all", "Homo sapiens")
mySrcUrls[[7]]<-"file:///home/cameron/microarray_data/annotate"
mySrcUrls[[2]]<-"file:///home/cameron/microarray_data/annotate/UniGene"
mySrcUrls[[4]]<-"file:///home/cameron/microarray_data/annotate/KEGG/path
ways"
 

myDir <- "/home/cameron/microarray_data/mwgAnnotate"
 

ABPkgBuilder( baseName=myBase, srcUrls=mySrcUrls,
baseMapType=myBaseType, pkgName="mwg40kA", pkgPath=myDir, organism="Homo
sapiens", version="0.10", author=list(authors="R. Cameron Craddock",
maintainer="R. Cameron Craddock <cmi5 at cdc.gov>"), fromWeb=TRUE)



Here is the output from ABPkgBuilder:

Attaching package: 'GO'
 
 
        The following object(s) are masked from package:AnnBuilder :
 
         GO
 
Read 1 item
Read 1 item
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00195.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00231.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00253.gene
   ...
   ...   ( removed a bunch of others )
   ...
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa07217.gene
[1] "4028 2 2"

The following data sets have been added to the database and will be
removed:
 [1]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAACCNUM.rd
a"
 [2]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kACHRLENGTH
S.rda"
 [3]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kACHRLOC.rd
a"
 [4]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAENZYME.rd
a"
 [5]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kALOCUSID.r
da"
 [6]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAMAPCOUNTS
.rda"
 [7]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAORGANISM.
rda"
 [8]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAPATH.rda"
 [9]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAPFAM.rda"
[10]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAPROSITE.r
da"
[11]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAQCDATA.rd
a"
[12]
"/home/cameron/microarray_data/mwgAnnotate/mwg40kA/data/mwg40kAQC.rda"

None of the files listed in the above warnings exist at the specified
location.  I verified this using ncftp.  After ABPkgBuilder finishes I
perform the following steps:

R CMD check mwg40kA/
(only warning is that data directory is empty)

R CMD build mwg40kA/
(no errors, no warnings)

R CMD INSTALL mwg30kA_0.10.tar.gz

* Installing *source* package 'mwg40kA' ...
** R
** data
**  moving datasets to lazyload DB
** help
 >>> Building/Updating help pages for package 'mwg40kA'
     Formats: text html latex example
  mwg40kA                           text    html    latex
  mwg40kAACCNUM                     text    html    latex   example
  mwg40kACHRLENGTHS                 text    html    latex   example
  mwg40kACHRLOC                     text    html    latex   example
  mwg40kAENZYME                     text    html    latex   example
  mwg40kALOCUSID                    text    html    latex   example
  mwg40kAORGANISM                   text    html    latex   example
  mwg40kAPATH                       text    html    latex   example
  mwg40kAPFAM                       text    html    latex   example
  mwg40kAPROSITE                    text    html    latex   example
  mwg40kAQC                         text    html    latex
  mwg40kAQCDATA                     text    html    latex
** building package indices ...
* DONE (mwg40kA)

This is what I get when I load the library:

> library(mwg40kA)
> mwg40kA()
 

 

Quality control information for  mwg40kA
Date built: Created: Tue Jul 25 16:48:06 2006
 

Number of probes: 20160
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         mwg40kAACCNUM found 19760 of 20160
         mwg40kACHRLOC found 0 of 20160
         mwg40kAENZYME found 0 of 20160
         mwg40kALOCUSID found 0 of 20160
         mwg40kAPATH found 0 of 20160
Mappings found for non-probe based rda files:
         mwg40kACHRLENGTHS found 25
         mwg40kAORGANISM found 1
         mwg40kAPFAM found 0
         mwg40kAPROSITE found 0
 

The mwg40kAACCNUM environment matches my basefile.  Can anyone suggest a
solution to my problem?

Thanks for your help,

Cameron