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@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


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