Rgraphviz windows version incompatible with current Graphviz
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Richard Gill ▴ 30
@richard-gill-4562
Last seen 9.6 years ago
Help! The current RGraphviz on windows requires graphviz-2.20.3. This is no longer available from the graphviz web pages, except as source code which you must build yourself. Does anyone have a better solution? Thanks in advance Richard Gill
Rgraphviz Rgraphviz • 767 views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
On 03/26/2011 06:37 AM, Richard Gill wrote: > Help! > > The current RGraphviz on windows requires graphviz-2.20.3. This is no > longer available from the graphviz web pages, except as source code > which you must build yourself. Does anyone have a better solution? Hi Richard -- The README file (see http://bioconductor.org/help/bioc- views/release/bioc/html/Rgraphviz.html for location, in the .tar.gz archive) says, correctly, that: o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1. msi in a directory that we'll call $DIR. We use the following as an example: C:\Graphviz2.20 If you install it in other dir, just use your dir correspondingly. o. Add Graphviz' bin diretory to the user PATH variable, e.g., c:\Graphviz2.20\bin o. Check the configuration by starting a new DOS window and displaying the PATH environment variable, e.g., c:\> echo %PATH% o. Use biocLite('Rgraphviz') to install Rgraphviz > > Thanks in advance > Richard Gill > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Dear Martin Thanks for your advice! This brings me a lot further. But shouldn't some of this info be contained on the 'front page" of Rgraphviz at bioconductor? If you install a windows binary you don't get to see a README file from the source package, and shouldn't have to expect, I think, that really crucial information is hidden there. Yours Richard > The README file (see > http://bioconductor.org/help/bioc- views/release/bioc/html/Rgraphviz.html for > location, in the .tar.gz archive) says, correctly, that: > > o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from > > > http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3. 1.msi >
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On 03/28/2011 10:50 AM, Richard Gill wrote: > Dear Martin > > Thanks for your advice! This brings me a lot further. > > But shouldn't some of this info be contained on the 'front page" of > Rgraphviz at bioconductor? If you install a windows binary you don't > get to see a README file from the source package, and shouldn't have > to expect, I think, that really crucial information is hidden there. I guess really we'd like the installation process to be painless. The landing page does say "Users on all platforms must install graphviz; see the README file, available in the source distribution of this file, for details." and loading Rgraphviz says, under recent R (2.12 for sure; I think 2.11 and maybe earlier), when unable to install, Check that (1) graphviz is installed on your system; (2) the installed version of graphviz matches '2.20.3'; this is the version used to build this Rgraphviz package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin' directory is in the system 'PATH' variable. See additional instructions in the 'README' file of the Rgraphviz 'source' distribution, available at http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask further questions on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html Martin > > Yours > Richard > > >> The README file (see >> http://bioconductor.org/help/bioc- views/release/bioc/html/Rgraphviz.html for >> location, in the .tar.gz archive) says, correctly, that: >> >> o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from >> >> >> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3 .1.msi >> -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Good point about the landing page. So you could have just said to me "RTFM!". Still, I'm working at a guest's desk in a foreign institute, with a PC which is not my own (I use mostly mac and sometimes linux). I even had to install 7zip to unpack the tar.gz file. Just in order to find a simple text file with a lot of *very* crucial information. Nowadays lazy people are used to installing first, asking questions later. (Still it isn't working but I think that's the fault of the local Windows system). R. -- Verstuurd vanaf mijn bevrijde aai-pet Sent from my jailbroken iPad On 28 Mar 2011, at 19:54, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 03/28/2011 10:50 AM, Richard Gill wrote: >> Dear Martin >> >> Thanks for your advice! This brings me a lot further. >> >> But shouldn't some of this info be contained on the 'front page" of >> Rgraphviz at bioconductor? If you install a windows binary you don't >> get to see a README file from the source package, and shouldn't have >> to expect, I think, that really crucial information is hidden there. > > I guess really we'd like the installation process to be painless. > > The landing page does say "Users on all platforms must install graphviz; see the README file, available in the source distribution of this file, for details." and loading Rgraphviz says, under recent R (2.12 for sure; I think 2.11 and maybe earlier), when unable to install, > > > Check that (1) graphviz is installed on your system; (2) > the installed version of graphviz matches '2.20.3'; this is > the version used to build this Rgraphviz package; (3) > graphviz is accessible to R, e.g., the path to the > graphviz 'bin' directory is in the system 'PATH' variable. > See additional instructions in the 'README' file of the > Rgraphviz 'source' distribution, available at > > http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html > > Ask further questions on the Bioconductor mailing list > > http://bioconductor.org/docs/mailList.html > > Martin > >> >> Yours >> Richard >> >> >>> The README file (see >>> http://bioconductor.org/help/bioc- views/release/bioc/html/Rgraphviz.html for >>> location, in the .tar.gz archive) says, correctly, that: >>> >>> o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from >>> >>> >>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20. 3.1.msi >>> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793
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I agree, it would be ideal if the Bioconductor webpages mirror README and INSTALL files from the top of the package. But it also needs to be implemented .... And you could argue who reads the webpage (for example, you seem to have missed the comment about reading the README file which already exists on the webpage). Now, I am not trying to be evasive about this. There is no doubt that Rgraphviz is one of the more hard-to-install packages in Bioconductor, especially for Windows. And we would certainly prefer the installation to be much more seamless. For example, we don't particular like that we are requiring an old version of Graphviz, but we have had problems with newer versions of GRaphviz on _some_ versions of Windows (for example, I think "we" can get Graphviz 2.26 to work under certain variants of 64 bit Windows, but it fails under other variants). In short, this package is really not trivial to get to work on all platforms. Now, I have been playing with the idea to experiment with bundling the source code of Graphviz with Rgraphviz. If one could get it to work (which is a big if, since GRaphviz is really meant to be build by Visual Studio), it would simplify the installation process greatly (and it would also solve the 64bit R on WIndows problem that may be getting hard to ignore). However, it is pretty non-trivial and would probably require as much as week or more of fulltime work for me (partly because of needing to use Windows) , something that I find hard to justify (especially since I am not really using Rgraphviz and certainly not Windows, myself). Of course, volunteers are always welcome. Kasper On Mon, Mar 28, 2011 at 1:50 PM, Richard Gill <gill1109 at="" gmail.com=""> wrote: > Dear Martin > > Thanks for your advice! This brings me a lot further. > > But shouldn't some of this info be contained on the 'front page" of > Rgraphviz at bioconductor? If you install a windows binary you don't > get to see a README file from the source package, and shouldn't have > to expect, I think, that really crucial information is hidden there. > > Yours > Richard > > >> The README file (see >> http://bioconductor.org/help/bioc- views/release/bioc/html/Rgraphviz.html for >> location, in the .tar.gz archive) says, correctly, that: >> >> o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from >> >> >> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3 .1.msi >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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