[BioC] AnnBuilder package
John Zhang
John Zhang <jzhang@jimmy.harvard.edu>
Thu, 28 Mar 2002 09:55:43 -0500 (EST)
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>Date: Thu, 28 Mar 2002 15:54:03 +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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>I just tried a 'R CMD check' to see if the doc could be built but could not go
through the check of examples....
The wwwfiles and temp folders were empty so that they do not get installed after
installation. I have put a dummy file in each to keep them alive. If you get the
latest versin of AnnBuilder, it should work.
>
>On Thu, Mar 28, 2002 at 09:24:41AM -0500, John Zhang wrote:
>>
>> >X-Authentication-Warning: giraffa.cbs.dtu.dk: laurent set sender to
>> laurent@genome.cbs.dtu.dk using -f
>> >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
>> >Mime-Version: 1.0
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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....
>> >
>> >
>> >
>> >
>> >
>> >
>> >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.
>>
>>
>> >
>> >
>> >I checked. There is no directory 'wwwfiles'.
>> >(note: I use R-devel)
>> >
>> >
>> >
>> >Thanks,
>> >
>> >
>> >
>> >
>> >Laurent
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >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
>> >> >X-BeenThere: bioconductor@stat.math.ethz.ch
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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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>> >
>> >--
>> >--------------------------------------------------------------
>> >other email: lgautier@altern.org
>> >--------------------------------------------------------------
>> >Laurent Gautier CBS, Building 208, DTU
>> >PhD. Student D-2800 Lyngby,Denmark
>> >tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
>
>--
>--------------------------------------------------------------
>other email: lgautier@altern.org
>--------------------------------------------------------------
>Laurent Gautier CBS, Building 208, DTU
>PhD. Student D-2800 Lyngby,Denmark
>tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent