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Question: .pdf files of GOstats documents
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gravatar for Shi, Tao
12.3 years ago by
Shi, Tao720
Shi, Tao720 wrote:
Hi All, 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, ...Tao --------------------------------- [[alternative HTML version deleted]]
ADD COMMENTlink modified 12.3 years ago by michael watson IAH-C3.4k • written 12.3 years ago by Shi, Tao720
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gravatar for Wolfgang Huber
12.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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? Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber
ADD COMMENTlink written 12.3 years ago by Wolfgang Huber13k
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
ADD REPLYlink written 12.3 years ago by Seth Falcon7.4k
Hi, Wolfgan: Thank you very much! The problem, I guess, is due to the lacking of "Rgraphviz" package, for which there is no windows version available for downloading. ...Tao Wolfgang Huber <huber@ebi.ac.uk> 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? Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber ------------------------------------- --------------------------------- [[alternative HTML version deleted]]
ADD REPLYlink written 12.3 years ago by Shi, Tao720
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gravatar for michael watson IAH-C
12.3 years ago by
michael watson IAH-C3.4k 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@stat.math.ethz.ch on behalf of Seth Falcon Sent: Tue 2/8/2005 9:34 PM To: bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.3 years ago by michael watson IAH-C3.4k
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@stat.math.ethz.ch on behalf of Seth Falcon >Sent: Tue 2/8/2005 9:34 PM >To: bioconductor@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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
ADD REPLYlink written 12.3 years ago by Steffen Moeller40
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gravatar for michael watson IAH-C
12.3 years ago by
michael watson IAH-C3.4k wrote:
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@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Steffen Moeller Sent: 09 February 2005 01:31 To: bioconductor@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@stat.math.ethz.ch on behalf of Seth Falcon >Sent: Tue 2/8/2005 9:34 PM >To: bioconductor@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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.3 years ago by michael watson IAH-C3.4k
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