[BioC] AnnBuilder package
John Zhang
John Zhang <jzhang@jimmy.harvard.edu>
Thu, 28 Mar 2002 09:24:41 -0500 (EST)
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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
>
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>Version 1.5.0 Under development (unstable) (2002-03-20)
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>> 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.
>
>
>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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