[BioC] AnnBuilder package

[John Zhang]

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>Date: Thu, 28 Mar 2002 15:15:10 +0100
>From: Laurent Gautier <laurent@genome.cbs.dtu.dk>
>To: John Zhang <jzhang@jimmy.harvard.edu>
>Subject: Re: [BioC] AnnBuilder package
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>Hello John,
>
>
>I tried to build the doc but get an error... I must do something dumb somewhere 
but cannot figure out where....
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>giraffa[laurent]:/tmp/transfer/AnnBuilder/inst/docs> echo "library(tools); 
Sweave('AnnBuilder.Rnw')" | /usr/local/packages/bin/R --vanilla --no-save
>
>R : Copyright 2002, The R Development Core Team
>Version 1.5.0 Under development (unstable) (2002-03-20)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type `license()' or `licence()' for distribution details.
>
>R is a collaborative project with many contributors.
>Type `contributors()' for more information.
>
>Type `demo()' for some demos, `help()' for on-line help, or
>`help.start()' for a HTML browser interface to help.
>Type `q()' to quit R.
>
>> library(tools); Sweave('AnnBuilder.Rnw')
>Writing to file AnnBuilder.tex
>Processing code chunks ...
> 1 : echo term verbatim (label=R)
> 2 : echo term verbatim (label=R)
> 3 : echo term verbatim (label=R)
> 4 : echo term verbatim (label=R)
>Error in download.file(srcURL, fileName, method = "internal", quiet = TRUE) : 
>	cannot open destfile 
`/usr/local/packages//lib/R/library/AnnBuilder/wwwfiles/Tll_tmpl.gz'
>Error in driver$runcode(drobj, chunk, chunkopts) : 
>	Error while evaluating chunk
>Execution halted

You may need to install AnnBuilder before running AnnBuilder.Rnw so that there 
is a wwwfiles folder under Annbuilder. Let me know if that still does work.


>
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>I checked. There is no directory 'wwwfiles'. 
>(note: I use R-devel)
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>Thanks,
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>Laurent
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>On Thu, Mar 28, 2002 at 08:27:44AM -0500, John Zhang wrote:
>> 
>> >From: Anthony Rossini <rossini@u.washington.edu>
>> >To: bioconductor@stat.math.ethz.ch
>> >MIME-Version: 1.0
>> >Subject: [BioC] AnnBuilder package
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>> >Date: Wed, 27 Mar 2002 12:54:02 -0800 (PST)
>> >
>> >I've taken a quick look, but is there a description for 
building/constructing 
>> the PostgreSQL schema in the package?  (I understand the R part, and could 
>> probably reverse-engineer w/o too much problems, but are there plans to 
provide 
>> a creation script for constructing the database?).
>> 
>> AnnBuilder.Rnw in AnnBuilder/inst/docs contains step by step instructions on 
how 
>> to build the annotation files. 
>> 
>> >Also, does the annotation builder have an "audit trail", i.e. a means of 
>> tracking changes in annotation records over time? 
>> 
>> No. But this is a very useful function to have. I will try to do something.
>>   
>> >
>> >Pointers to places in the directory structure/functions to look at are 
welcome.
>> >
>> >
>> >best,
>> >-tony
>> >
>> >----
>> >A.J. Rossini                            Rsrch Asst Professor of 
Biostatistics
>> >rossini@u.washington.edu                
http://software.biostat.washington.edu/
>> >Biostatistics/Univ. of Washington       206-543-1044 (3286=fax) (Thursdays)
>> >HIV Vaccine Trials Network/FHCRC        206-667-7025 (4812=fax) (M/Tu/W)
>> >(Friday location is generally unknown).
>> >
>> >
>> >
>> >
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>-- 
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>Laurent Gautier			CBS, Building 208, DTU
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