[BioC] .pdf files of GOstats documents

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Feb 9 10:05:35 CET 2005 

Sorry, I forgot to mention this is on Windows, which has been flagged up
as being due to the absence of Rgraphviz

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Steffen
Moeller
Sent: 09 February 2005 01:31
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] .pdf files of GOstats documents


I recently compiled 1.1.2 on Debian Linux and it seems all fine for me.

The following files I get

dpkg -c ../../gostats/r-bioconductor-gostats_1.1.2-1_all.deb|grep pdf
-rw-r--r-- root/root     23100 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-tfGplot.pdf
-rw-r--r-- root/root      3569 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-GO2LL.pdf
-rw-r--r-- root/root     20664 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-GOg1.pdf
-rw-r--r-- root/root     21614 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-GOxx.pdf
-rw-r--r-- root/root      3457 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/fig_histabsdiff.pdf
-rw-r--r-- root/root     34992 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-pathPairs.pdf
-rw-r--r-- root/root      8471 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-pathinNEG.pdf
-rw-r--r-- root/root      8841 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats-pathinB.pdf
-rw-r--r-- root/root    272551 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOstats.pdf
-rw-r--r-- root/root     80744 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOusage.pdf
-rw-r--r-- root/root     86928 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOvis-GOMF.pdf
-rw-r--r-- root/root    227770 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOvis-GOBP.pdf
-rw-r--r-- root/root     27424 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOvis-GOCC.pdf
-rw-r--r-- root/root    434896 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/GOvis.pdf

At least GOvis.pdf and GOstats.pdf are fine with xpdf.

$ dpkg -c r-bioconductor-gostats_1.1.2-1_all.deb|grep html
-rw-r--r-- root/root      5183 2005-02-08 19:45:58 
./usr/lib/R/site-library/GOstats/doc/example.html
-rw-r--r-- root/root       386 2005-02-08 19:46:45 
./usr/lib/R/site-library/GOstats/doc/index.html
drwxr-xr-x root/root         0 2005-02-08 19:46:38 
./usr/lib/R/site-library/GOstats/html/
-rw-r--r-- root/root      4721 2005-02-08 19:46:29 
./usr/lib/R/site-library/GOstats/html/00Index.html
-rw-r--r-- root/root      3390 2005-02-08 19:46:32 
./usr/lib/R/site-library/GOstats/html/ALL.html
-rw-r--r-- root/root      4380 2005-02-08 19:46:33 
./usr/lib/R/site-library/GOstats/html/GOHyperG.html
-rw-r--r-- root/root      1538 2005-02-08 19:46:33 
./usr/lib/R/site-library/GOstats/html/GOLeaves.html
-rw-r--r-- root/root      1004 2005-02-08 19:46:33 
./usr/lib/R/site-library/GOstats/html/GOstats-defunct.html
-rw-r--r-- root/root      1077 2005-02-08 19:46:33 
./usr/lib/R/site-library/GOstats/html/Ndists.html
-rw-r--r-- root/root      2240 2005-02-08 19:46:34 
./usr/lib/R/site-library/GOstats/html/compCorrGraph.html
-rw-r--r-- root/root      1938 2005-02-08 19:46:34 
./usr/lib/R/site-library/GOstats/html/compGdist.html
-rw-r--r-- root/root      1982 2005-02-08 19:46:34 
./usr/lib/R/site-library/GOstats/html/dropECode.html
-rw-r--r-- root/root      1414 2005-02-08 19:46:34 
./usr/lib/R/site-library/GOstats/html/getEvidence.html
-rw-r--r-- root/root      2775 2005-02-08 19:46:35 
./usr/lib/R/site-library/GOstats/html/getGOTerm.html
-rw-r--r-- root/root      1938 2005-02-08 19:46:35 
./usr/lib/R/site-library/GOstats/html/getOntology.html
-rw-r--r-- root/root      1524 2005-02-08 19:46:35 
./usr/lib/R/site-library/GOstats/html/hasGOannote.html
-rw-r--r-- root/root      1663 2005-02-08 19:46:36 
./usr/lib/R/site-library/GOstats/html/idx2dimnames.html
-rw-r--r-- root/root      2213 2005-02-08 19:46:36 
./usr/lib/R/site-library/GOstats/html/makeGOGraph.html
-rw-r--r-- root/root      1536 2005-02-08 19:46:36 
./usr/lib/R/site-library/GOstats/html/notConn.html
-rw-r--r-- root/root      2047 2005-02-08 19:46:36 
./usr/lib/R/site-library/GOstats/html/oneGOGraph.html
-rw-r--r-- root/root      3062 2005-02-08 19:46:37 
./usr/lib/R/site-library/GOstats/html/shortestPath.html
-rw-r--r-- root/root      3443 2005-02-08 19:46:37 
./usr/lib/R/site-library/GOstats/html/simLL.html
-rw-r--r-- root/root      3067 2005-02-08 19:46:38 
./usr/lib/R/site-library/GOstats/html/triadCensus.html


Many greetings

Steffen


michael watson (IAH-C) wrote:

>I raised this a few days ago - the GOStats documentation is only 
>partially there in my installation too.  A bit of an html file, the 
>start of a tex document etc
>
>
>-----Original Message-----
>From:	bioconductor-bounces at stat.math.ethz.ch on behalf of Seth Falcon
>Sent:	Tue 2/8/2005 9:34 PM
>To:	bioconductor at stat.math.ethz.ch
>Cc:	
>Subject:	Re: [BioC] .pdf files of GOstats documents
>
>On Tue, Feb 08, 2005 at 10:08:53PM -0800, Wolfgang Huber wrote:
>  
>
>>Hi Shi, Tao
>>
>>    
>>
>>>After the installation of GOstats (1.1.1) library to R (2.0.1, 
>>>windows2K),
>>>I don't see the .pdf vignettes in the GOstats/doc/ directory.  I've
been 
>>>having trouble in converting the .Rnw files to .tex and to .pdf file.
I 
>>>would really appreciate if somebody can send me these .pdf files or
tell 
>>>me where to get them.  Thank you,
>>>
>>>      
>>>
>>http://www.bioconductor.org/
>>  click on "vignettes",
>>  click on the one you want.
>>
>>But normally the vignettes should come with the package - what went 
>>wrong?
>>    
>>
>
>I'm not sure yet, but we will look into it.  The vignettes should be 
>included.
>
>+ seth
>
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>  
>

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