Rgraphviz, R 2.7.0 and Windows XP
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@myroslav-sypa-2832
Last seen 10.2 years ago
Hello all, I'm creating an application which use rJava to connect with R. But my question is about Rgraphviz. Could you tell me if Rgraphviz will (in nearest future) work with R 2.7.0 as it has been working with R 2.6.*? I mean that for installing Rgraphviz I need just run these two strings in R: /source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") /?/ / -- Best regards, Myroslav
Rgraphviz Rgraphviz • 2.2k views
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 5 months ago
United States
Hi Tony, Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, and I've tried two different Windows machines. I'm not sure the problem completely lies with Rgraphviz, but maybe with Graphviz as well. Even though I want to use the Rgraphviz Windows binary instead of building Rgraphviz, I followed the README file found in the Rgraphviz_1.18.1.tar.gz source file: 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft Visual C++ 2005 SP1 Redistributable Package", but I downloaded and installed the package from the link provided, following all their instructions and warnings. 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from Graphviz.org, which is the only 2.16 version available. 3. I created the new user variables as indicated, and made sure the C:\Program Files\graphviz-2.16\bin was added to my path (it was done automatically) 4. Then I used biocLite() to install Rgraphviz. When I tried to load Rgraphviz, I got both a Windows error and an error within R; The Windows error message is known to Graphviz because it is mentioned on the download page: "The application has failed to start because somefilename.dll was not found. Re-installing the application may fix this problem." Graphviz says to install Microsoft Visual C++ 2005 Redistributable Package (x86) to fix it, but I've already done that! The R error message is: > library(Rgraphviz) Loading required package: grid Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' Finally, I finished the directions in the README file to safely load Rgraphviz but I got another error message: > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/Program Files/graphviz-2.16/bin/gvc.dll': LoadLibrary failure: The specified module could not be found. So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz from source have created it? I'm still having the general Windows problem related to the Microsoft Visual C++ 2005 Redistributable Package (x86), which I have no idea how to fix. I'd be very interested in hearing if anyone has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 and how they did it. If someone knows what I'm doing wrong or have other suggestions to try, please let me now! Overall, I doubt that a generic/novice Windows R user could be able to get Rgraphviz to work... Thanks, Jenny > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid splines tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 loaded via a namespace (and not attached): [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > At 10:39 AM 6/3/2008, Tony Chiang wrote: >I am sure that there are plenty of folks with Windows XP and R-2.7.0 who >have gotten Rgraphviz to work. Unless you let us who what seems to be the >problem on your end, I would suggest reading the large number of e-mails >from the archives that deals with the different issues that have come >up...and maybe it might solve your problems. > >tony > >On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at="" email.unc.edu=""> wrote: > > > Hello all, > > > > I'm creating an application which use rJava to connect with R. But my > > question is about Rgraphviz. Could you tell me if Rgraphviz will > (in nearest > > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean that > > for installing Rgraphviz I need just run these two strings in R: > > > > /source("http://bioconductor.org/biocLite.R") > > biocLite("Rgraphviz") > > > > /?/ > > / > > > > -- > > Best regards, Myroslav > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
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I'm a little reluctant to add my comments here, which seem to miss the mark more often than not on this, but.. Jenny Drnevich wrote: > Hi Tony, > > Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, > and I've tried two different Windows machines. I'm not sure the problem > completely lies with Rgraphviz, but maybe with Graphviz as well. Even > though I want to use the Rgraphviz Windows binary instead of building > Rgraphviz, I followed the README file found in the > Rgraphviz_1.18.1.tar.gz source file: > > 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft > Visual C++ 2005 SP1 Redistributable Package", but I downloaded and > installed the package from the link provided, following all their > instructions and warnings. > > 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from > Graphviz.org, which is the only 2.16 version available. Actually, you don't want this static version. Instead go looking here http://www.graphviz.org/pub/graphviz/ARCHIVE/ Make sure to clean up as completely as possible your previous installation. I *think*, contrary to previous posts of mine, that you can also use the recent graphviz (2.18), so long as you're building Rgraphviz yourself. Once built, your Rgraphviz will still have missing functionality, in particular it will be unable to read / write graph objects using agopen, agwrite, etc. This seems to be a complex issue in the interaction between R and graphviz, tracing I think to the use of different development tools for the two project. There might be similar surprises in other functions; these are just the ones that the Bioc build machine stumbles on when checking the package. You'll encounter missing functionality in a most unpleasant way, abruptly aborting your session. I think the rationale for not updating the instructions in the package, or making some functionality 'optional' on windows, is the hope for a more robust solution. Again I seem to have a poor track record on providing reliable information about this, so please take with a grain of salt. Martin > 3. I created the new user variables as indicated, and made sure the > C:\Program Files\graphviz-2.16\bin was added to my path (it was done > automatically) > > 4. Then I used biocLite() to install Rgraphviz. > > When I tried to load Rgraphviz, I got both a Windows error and an error > within R; The Windows error message is known to Graphviz because it is > mentioned on the download page: "The application has failed to start > because somefilename.dll was not found. Re-installing the application > may fix this problem." Graphviz says to install Microsoft Visual C++ > 2005 Redistributable Package (x86) to fix it, but I've already done that! > > The R error message is: > > library(Rgraphviz) > Loading required package: grid > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': > LoadLibrary failure: The specified module could not be found. > > > Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > > Finally, I finished the directions in the README file to safely load > Rgraphviz but I got another error message: > > > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library 'C:/Program > Files/graphviz-2.16/bin/gvc.dll': > LoadLibrary failure: The specified module could not be found. > > > So is this gvc.dll file missing from Graphviz? Or would building > Rgraphviz from source have created it? I'm still having the general > Windows problem related to the Microsoft Visual C++ 2005 Redistributable > Package (x86), which I have no idea how to fix. I'd be very interested > in hearing if anyone has gotten the Rgraphviz Windows _binary_ working > with R 2.7.0 and how they did it. If someone knows what I'm doing wrong > or have other suggestions to try, please let me now! Overall, I doubt > that a generic/novice Windows R user could be able to get Rgraphviz to > work... > > Thanks, > Jenny > > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid splines tools stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 > [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 > [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 > [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 > [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 > [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 > [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 > [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 > [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > > > > > > > At 10:39 AM 6/3/2008, Tony Chiang wrote: >> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who >> have gotten Rgraphviz to work. Unless you let us who what seems to be the >> problem on your end, I would suggest reading the large number of e-mails >> from the archives that deals with the different issues that have come >> up...and maybe it might solve your problems. >> >> tony >> >> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at="" email.unc.edu=""> >> wrote: >> >> > Hello all, >> > >> > I'm creating an application which use rJava to connect with R. But my >> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in >> nearest >> > future) work with R 2.7.0 as it has been working with R 2.6.*? I >> mean that >> > for installing Rgraphviz I need just run these two strings in R: >> > >> > /source("http://bioconductor.org/biocLite.R") >> > biocLite("Rgraphviz") >> > >> > /?/ >> > / >> > >> > -- >> > Best regards, Myroslav >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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Hi Martin et al, On Tue, Jun 3, 2008 at 7:36 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > I'm a little reluctant to add my comments here, which seem to miss the mark > more often than not on this, but.. > > Jenny Drnevich wrote: > >> Hi Tony, >> >> Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, and >> I've tried two different Windows machines. I'm not sure the problem >> completely lies with Rgraphviz, but maybe with Graphviz as well. Even though >> I want to use the Rgraphviz Windows binary instead of building Rgraphviz, I >> followed the README file found in the Rgraphviz_1.18.1.tar.gz source file: >> >> 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft >> Visual C++ 2005 SP1 Redistributable Package", but I downloaded and installed >> the package from the link provided, following all their instructions and >> warnings. >> >> 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from >> Graphviz.org, which is the only 2.16 version available. >> > > Actually, you don't want this static version. Instead go looking here > > http://www.graphviz.org/pub/graphviz/ARCHIVE/ > > Make sure to clean up as completely as possible your previous installation. > > I *think*, contrary to previous posts of mine, that you can also use the > recent graphviz (2.18), so long as you're building Rgraphviz yourself. > At least on my Macbook pro, this is true (at least it works for me without failing). Jenny, if you use biocLite, make sure that you set the type="source" to build it from source. > > Once built, your Rgraphviz will still have missing functionality, in > particular it will be unable to read / write graph objects using agopen, > agwrite, etc. This seems to be a complex issue in the interaction between R > and graphviz, tracing I think to the use of different development tools for > the two project. There might be similar surprises in other functions; these > are just the ones that the Bioc build machine stumbles on when checking the > package. You'll encounter missing functionality in a most unpleasant way, > abruptly aborting your session. > I don't have access to a windows machine at the moment, but this also happened on my mac a few months back (always with the agopen and agwrite). After I grab the lastest X-code (with the latest compliers) and built both graphviz and Rgraphviz from source on the (also following Martin's advice to make sure that all previous incarnations of graphviz were completely removed before building graphviz again), this problem seems to have gone away. > > I think the rationale for not updating the instructions in the package, or > making some functionality 'optional' on windows, is the hope for a more > robust solution. > > Again I seem to have a poor track record on providing reliable information > about this, so please take with a grain of salt. > I should say ditto for me too now! > > Martin > > > 3. I created the new user variables as indicated, and made sure the >> C:\Program Files\graphviz-2.16\bin was added to my path (it was done >> automatically) >> >> 4. Then I used biocLite() to install Rgraphviz. >> >> When I tried to load Rgraphviz, I got both a Windows error and an error >> within R; The Windows error message is known to Graphviz because it is >> mentioned on the download page: "The application has failed to start because >> somefilename.dll was not found. Re-installing the application may fix this >> problem." Graphviz says to install Microsoft Visual C++ 2005 >> Redistributable Package (x86) to fix it, but I've already done that! >> >> The R error message is: >> > library(Rgraphviz) >> Loading required package: grid >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': >> LoadLibrary failure: The specified module could not be found. >> >> >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' >> Error: package/namespace load failed for 'Rgraphviz' >> >> >> Finally, I finished the directions in the README file to safely load >> Rgraphviz but I got another error message: >> >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library 'C:/Program >> Files/graphviz-2.16/bin/gvc.dll': >> LoadLibrary failure: The specified module could not be found. >> >> >> So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz >> from source have created it? I'm still having the general Windows problem >> related to the Microsoft Visual C++ 2005 Redistributable Package (x86), >> which I have no idea how to fix. I'd be very interested in hearing if anyone >> has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 and how they >> did it. If someone knows what I'm doing wrong or have other suggestions to >> try, please let me now! Overall, I doubt that a generic/novice Windows R >> user could be able to get Rgraphviz to work... >> >> Thanks, >> Jenny >> >> > sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid splines tools stats graphics grDevices utils >> [8] datasets methods base >> >> other attached packages: >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 >> > >> >> >> >> >> At 10:39 AM 6/3/2008, Tony Chiang wrote: >> >>> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who >>> have gotten Rgraphviz to work. Unless you let us who what seems to be the >>> problem on your end, I would suggest reading the large number of e-mails >>> from the archives that deals with the different issues that have come >>> up...and maybe it might solve your problems. >>> >>> tony >>> >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa@email.unc.edu> >>> wrote: >>> >>> > Hello all, >>> > >>> > I'm creating an application which use rJava to connect with R. But my >>> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in >>> nearest >>> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean >>> that >>> > for installing Rgraphviz I need just run these two strings in R: >>> > >>> > /source("http://bioconductor.org/biocLite.R") >>> > biocLite("Rgraphviz") >>> > >>> > /?/ >>> > / >>> > >>> > -- >>> > Best regards, Myroslav >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor@stat.math.ethz.ch >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > Search the archives: >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> Jenny Drnevich, Ph.D. >> >> Functional Genomics Bioinformatics Specialist >> W.M. Keck Center for Comparative and Functional Genomics >> Roy J. Carver Biotechnology Center >> University of Illinois, Urbana-Champaign >> >> 330 ERML >> 1201 W. Gregory Dr. >> Urbana, IL 61801 >> USA >> >> ph: 217-244-7355 >> fax: 217-265-5066 >> e-mail: drnevich@illinois.edu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
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I'm even more reluctant to chime in, but... There are enough variables here that it seems a case could be made for making the graphviz dlls/shared libraries compatible with the BioC binary packages of Rgraphviz available on an applicable website to be copied into the lib directory of Rgraphviz. Since graphviz is freely redistributable, this would simplify things for some users of the binary packages. There are reasons for not doing this, of course. But it seems likely that this is going to become/continue to be a recurrent theme without the shortcut. -Eric > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Tony Chiang > Sent: Tuesday, June 03, 2008 2:58 PM > To: Martin Morgan > Cc: Jenny Drnevich; Myroslav Sypa; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Rgraphviz, R 2.7.0 and Windows XP > > > Hi Martin et al, > > On Tue, Jun 3, 2008 at 7:36 PM, Martin Morgan > <mtmorgan at="" fhcrc.org=""> wrote: > > > I'm a little reluctant to add my comments here, which seem > to miss the > > mark more often than not on this, but.. > > > > Jenny Drnevich wrote: > > > >> Hi Tony, > >> > >> Actually, I have NOT been able to get Rgraphviz to work > with R 2.7.0, > >> and I've tried two different Windows machines. I'm not sure the > >> problem completely lies with Rgraphviz, but maybe with Graphviz as > >> well. Even though I want to use the Rgraphviz Windows > binary instead > >> of building Rgraphviz, I followed the README file found in the > >> Rgraphviz_1.18.1.tar.gz source file: > >> > >> 1. I'm not sure how to "make sure your MSVCR80.DLL is from > Microsoft > >> Visual C++ 2005 SP1 Redistributable Package", but I downloaded and > >> installed the package from the link provided, following all their > >> instructions and warnings. > >> > >> 2. I downloaded and installed the > graphviz-2.16.1.static.exe binary > >> from Graphviz.org, which is the only 2.16 version available. > >> > > > > Actually, you don't want this static version. Instead go > looking here > > > > http://www.graphviz.org/pub/graphviz/ARCHIVE/ > > > > Make sure to clean up as completely as possible your previous > > installation. > > > > I *think*, contrary to previous posts of mine, that you can > also use > > the recent graphviz (2.18), so long as you're building Rgraphviz > > yourself. > > > > At least on my Macbook pro, this is true (at least it works > for me without failing). Jenny, if you use biocLite, make > sure that you set the type="source" to build it from source. > > > > > > Once built, your Rgraphviz will still have missing > functionality, in > > particular it will be unable to read / write graph objects using > > agopen, agwrite, etc. This seems to be a complex issue in the > > interaction between R and graphviz, tracing I think to the use of > > different development tools for the two project. There might be > > similar surprises in other functions; these are just the > ones that the > > Bioc build machine stumbles on when checking the package. You'll > > encounter missing functionality in a most unpleasant way, abruptly > > aborting your session. > > > > I don't have access to a windows machine at the moment, but > this also happened on my mac a few months back (always with > the agopen and agwrite). After I grab the lastest X-code > (with the latest compliers) and built both graphviz and > Rgraphviz from source on the (also following Martin's advice > to make sure that all previous incarnations of graphviz were > completely removed before building graphviz again), this > problem seems to have gone away. > > > > > > I think the rationale for not updating the instructions in the > > package, or making some functionality 'optional' on windows, is the > > hope for a more robust solution. > > > > Again I seem to have a poor track record on providing reliable > > information about this, so please take with a grain of salt. > > > > I should say ditto for me too now! > > > > > > Martin > > > > > > 3. I created the new user variables as indicated, and made sure the > >> C:\Program Files\graphviz-2.16\bin was added to my path > (it was done > >> automatically) > >> > >> 4. Then I used biocLite() to install Rgraphviz. > >> > >> When I tried to load Rgraphviz, I got both a Windows error and an > >> error within R; The Windows error message is known to Graphviz > >> because it is mentioned on the download page: "The application has > >> failed to start because somefilename.dll was not found. > Re-installing > >> the application may fix this problem." Graphviz says to install > >> Microsoft Visual C++ 2005 Redistributable Package (x86) to fix it, > >> but I've already done that! > >> > >> The R error message is: > >> > library(Rgraphviz) > >> Loading required package: grid > >> Error in inDL(x, as.logical(local), as.logical(now), ...) > : unable > >> to load shared library > >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > >> Error: package/namespace load failed for 'Rgraphviz' > >> > >> > >> Finally, I finished the directions in the README file to > safely load > >> Rgraphviz but I got another error message: > >> > >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") Error in > >> inDL(x, as.logical(local), as.logical(now), ...) : unable to load > >> shared library 'C:/Program > >> Files/graphviz-2.16/bin/gvc.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> So is this gvc.dll file missing from Graphviz? Or would building > >> Rgraphviz from source have created it? I'm still having > the general > >> Windows problem related to the Microsoft Visual C++ 2005 > >> Redistributable Package (x86), which I have no idea how to > fix. I'd > >> be very interested in hearing if anyone has gotten the Rgraphviz > >> Windows _binary_ working with R 2.7.0 and how they did it. > If someone > >> knows what I'm doing wrong or have other suggestions to > try, please > >> let me now! Overall, I doubt that a generic/novice Windows R user > >> could be able to get Rgraphviz to work... > >> > >> Thanks, > >> Jenny > >> > >> > sessionInfo() > >> R version 2.7.0 (2008-04-22) > >> i386-pc-mingw32 > >> > >> locale: > >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > >> States.1252;LC_MONETARY=English_United > >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >> > >> attached base packages: > >> [1] grid splines tools stats graphics > grDevices utils > >> [8] datasets methods base > >> > >> other attached packages: > >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 > >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 > >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 > >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 > >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 > >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 > >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 > >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 > >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 > >> > >> loaded via a namespace (and not attached): > >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > >> > > >> > >> > >> > >> > >> At 10:39 AM 6/3/2008, Tony Chiang wrote: > >> > >>> I am sure that there are plenty of folks with Windows XP > and R-2.7.0 > >>> who have gotten Rgraphviz to work. Unless you let us who > what seems > >>> to be the problem on your end, I would suggest reading the large > >>> number of e-mails from the archives that deals with the different > >>> issues that have come up...and maybe it might solve your problems. > >>> > >>> tony > >>> > >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa > <msypa at="" email.unc.edu=""> > >>> wrote: > >>> > >>> > Hello all, > >>> > > >>> > I'm creating an application which use rJava to connect > with R. But > >>> > my question is about Rgraphviz. Could you tell me if Rgraphviz > >>> > will (in > >>> nearest > >>> > future) work with R 2.7.0 as it has been working with R > 2.6.*? I > >>> > mean > >>> that > >>> > for installing Rgraphviz I need just run these two strings in R: > >>> > > >>> > /source("http://bioconductor.org/biocLite.R") > >>> > biocLite("Rgraphviz") > >>> > > >>> > /?/ > >>> > / > >>> > > >>> > -- > >>> > Best regards, Myroslav > >>> > > >>> > _______________________________________________ > >>> > Bioconductor mailing list > >>> > Bioconductor at stat.math.ethz.ch > >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > Search the archives: > >>> > > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > >> Jenny Drnevich, Ph.D. > >> > >> Functional Genomics Bioinformatics Specialist > >> W.M. Keck Center for Comparative and Functional Genomics > >> Roy J. Carver Biotechnology Center > >> University of Illinois, Urbana-Champaign > >> > >> 330 ERML > >> 1201 W. Gregory Dr. > >> Urbana, IL 61801 > >> USA > >> > >> ph: 217-244-7355 > >> fax: 217-265-5066 > >> e-mail: drnevich at illinois.edu > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > -- > > Martin Morgan > > Computational Biology / Fred Hutchinson Cancer Research Center 1100 > > Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M2 B169 > > Phone: (206) 667-2793 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > This email message, including any attachments, is for th...{{dropped:6}}
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Hi Jenny, Someone had the same error and posted the question to the mailing list. Martin had a suggestion about setting the path correctly (as Li also mentioned). Here is Martin's reply: The Rgraphviz currently available for Windows with biocLite is built > with graphviz 2.16, so you'll need to install > > http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz > -win-2.16.1.bin.tar.gz > > Likely the problem you have below is because the path to graphviz > needs to be added to your system PATH variable, e.g., settings -> control > panels -> system -> advanced -> Environment Variables and then adding > or editing a variable PATH to contain the path to graphviz' bin > directory. My path reads in part > > C:\Program Files\Graphviz2.16\Bin > > The version of graphviz installed on your computer has to match the > version used to build Rgraphviz, so 2.18 will not work. > > Martin I use google mail, so I can search in my folders for past post fairly easily. There are quite a few posts about Rgraphviz, and I understand it has been hard for people to get things working. I use a mac almost exclusively, and had a rough time with it as well. But searching the archives and (if there is no reasonable answers there) letting us know what went wrong will let us better help. cheers, --tony On Tue, Jun 3, 2008 at 7:14 PM, Jenny Drnevich <drnevich@illinois.edu> wrote: > Hi Tony, > > Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, and > I've tried two different Windows machines. I'm not sure the problem > completely lies with Rgraphviz, but maybe with Graphviz as well. Even though > I want to use the Rgraphviz Windows binary instead of building Rgraphviz, I > followed the README file found in the Rgraphviz_1.18.1.tar.gz source file: > > 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft Visual > C++ 2005 SP1 Redistributable Package", but I downloaded and installed the > package from the link provided, following all their instructions and > warnings. > > 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from > Graphviz.org, which is the only 2.16 version available. > > 3. I created the new user variables as indicated, and made sure the > C:\Program Files\graphviz-2.16\bin was added to my path (it was done > automatically) > > 4. Then I used biocLite() to install Rgraphviz. > > When I tried to load Rgraphviz, I got both a Windows error and an error > within R; The Windows error message is known to Graphviz because it is > mentioned on the download page: "The application has failed to start because > somefilename.dll was not found. Re-installing the application may fix this > problem." Graphviz says to install Microsoft Visual C++ 2005 > Redistributable Package (x86) to fix it, but I've already done that! > > The R error message is: > > library(Rgraphviz) > Loading required package: grid > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': > LoadLibrary failure: The specified module could not be found. > > > Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > > Finally, I finished the directions in the README file to safely load > Rgraphviz but I got another error message: > > > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library 'C:/Program > Files/graphviz-2.16/bin/gvc.dll': > LoadLibrary failure: The specified module could not be found. > > > So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz > from source have created it? I'm still having the general Windows problem > related to the Microsoft Visual C++ 2005 Redistributable Package (x86), > which I have no idea how to fix. I'd be very interested in hearing if anyone > has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 and how they > did it. If someone knows what I'm doing wrong or have other suggestions to > try, please let me now! Overall, I doubt that a generic/novice Windows R > user could be able to get Rgraphviz to work... > > Thanks, > Jenny > > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid splines tools stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 > [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 > [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 > [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 > [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 > [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 > [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 > [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 > [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > > > > > > > > At 10:39 AM 6/3/2008, Tony Chiang wrote: > >> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who >> have gotten Rgraphviz to work. Unless you let us who what seems to be the >> problem on your end, I would suggest reading the large number of e-mails >> from the archives that deals with the different issues that have come >> up...and maybe it might solve your problems. >> >> tony >> >> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa@email.unc.edu> >> wrote: >> >> > Hello all, >> > >> > I'm creating an application which use rJava to connect with R. But my >> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in >> nearest >> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean >> that >> > for installing Rgraphviz I need just run these two strings in R: >> > >> > /source("http://bioconductor.org/biocLite.R") >> > biocLite("Rgraphviz") >> > >> > /?/ >> > / >> > >> > -- >> > Best regards, Myroslav >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
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Sorry Jenny, I forgot to ask...you mention that you were using Rgraphviz_1.18.1 but then say you installed 2.16.1, why is that? On Tue, Jun 3, 2008 at 7:27 PM, Tony Chiang <tchiang@fhcrc.org> wrote: > Hi Jenny, > > Someone had the same error and posted the question to the mailing list. > Martin had a suggestion about setting the path correctly (as Li also > mentioned). Here is Martin's reply: > > The Rgraphviz currently available for Windows with biocLite is built >> with graphviz 2.16, so you'll need to install >> >> http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz >> -win-2.16.1.bin.tar.gz >> >> Likely the problem you have below is because the path to graphviz >> needs to be added to your system PATH variable, e.g., settings -> control >> panels -> system -> advanced -> Environment Variables and then adding >> or editing a variable PATH to contain the path to graphviz' bin >> directory. My path reads in part >> >> C:\Program Files\Graphviz2.16\Bin >> >> The version of graphviz installed on your computer has to match the >> version used to build Rgraphviz, so 2.18 will not work. >> >> Martin > > > I use google mail, so I can search in my folders for past post fairly > easily. There are quite a few posts about Rgraphviz, and I understand it has > been hard for people to get things working. I use a mac almost exclusively, > and had a rough time with it as well. > > But searching the archives and (if there is no reasonable answers there) > letting us know what went wrong will let us better help. > > cheers, > --tony > > On Tue, Jun 3, 2008 at 7:14 PM, Jenny Drnevich <drnevich@illinois.edu> > wrote: > >> Hi Tony, >> >> Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, and >> I've tried two different Windows machines. I'm not sure the problem >> completely lies with Rgraphviz, but maybe with Graphviz as well. Even though >> I want to use the Rgraphviz Windows binary instead of building Rgraphviz, I >> followed the README file found in the Rgraphviz_1.18.1.tar.gz source file: >> >> 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft >> Visual C++ 2005 SP1 Redistributable Package", but I downloaded and installed >> the package from the link provided, following all their instructions and >> warnings. >> >> 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from >> Graphviz.org, which is the only 2.16 version available. >> >> 3. I created the new user variables as indicated, and made sure the >> C:\Program Files\graphviz-2.16\bin was added to my path (it was done >> automatically) >> >> 4. Then I used biocLite() to install Rgraphviz. >> >> When I tried to load Rgraphviz, I got both a Windows error and an error >> within R; The Windows error message is known to Graphviz because it is >> mentioned on the download page: "The application has failed to start because >> somefilename.dll was not found. Re-installing the application may fix this >> problem." Graphviz says to install Microsoft Visual C++ 2005 >> Redistributable Package (x86) to fix it, but I've already done that! >> >> The R error message is: >> > library(Rgraphviz) >> Loading required package: grid >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': >> LoadLibrary failure: The specified module could not be found. >> >> >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' >> Error: package/namespace load failed for 'Rgraphviz' >> >> >> Finally, I finished the directions in the README file to safely load >> Rgraphviz but I got another error message: >> >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library 'C:/Program >> Files/graphviz-2.16/bin/gvc.dll': >> LoadLibrary failure: The specified module could not be found. >> >> >> So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz >> from source have created it? I'm still having the general Windows problem >> related to the Microsoft Visual C++ 2005 Redistributable Package (x86), >> which I have no idea how to fix. I'd be very interested in hearing if anyone >> has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 and how they >> did it. If someone knows what I'm doing wrong or have other suggestions to >> try, please let me now! Overall, I doubt that a generic/novice Windows R >> user could be able to get Rgraphviz to work... >> >> Thanks, >> Jenny >> >> > sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid splines tools stats graphics grDevices utils >> [8] datasets methods base >> >> other attached packages: >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 >> >> > >> >> >> >> >> At 10:39 AM 6/3/2008, Tony Chiang wrote: >> >>> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who >>> have gotten Rgraphviz to work. Unless you let us who what seems to be the >>> problem on your end, I would suggest reading the large number of e-mails >>> from the archives that deals with the different issues that have come >>> up...and maybe it might solve your problems. >>> >>> tony >>> >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa@email.unc.edu> >>> wrote: >>> >>> > Hello all, >>> > >>> > I'm creating an application which use rJava to connect with R. But my >>> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in >>> nearest >>> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean >>> that >>> > for installing Rgraphviz I need just run these two strings in R: >>> > >>> > /source("http://bioconductor.org/biocLite.R") >>> > biocLite("Rgraphviz") >>> > >>> > /?/ >>> > / >>> > >>> > -- >>> > Best regards, Myroslav >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor@stat.math.ethz.ch >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > Search the archives: >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> Jenny Drnevich, Ph.D. >> >> Functional Genomics Bioinformatics Specialist >> W.M. Keck Center for Comparative and Functional Genomics >> Roy J. Carver Biotechnology Center >> University of Illinois, Urbana-Champaign >> >> 330 ERML >> 1201 W. Gregory Dr. >> Urbana, IL 61801 >> USA >> >> ph: 217-244-7355 >> fax: 217-265-5066 >> e-mail: drnevich@illinois.edu >> > > [[alternative HTML version deleted]]
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 5 months ago
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Hi Tony, I got your other e-mail - thanks for working on trying to figure out what's wrong. For others following this post, there is a lot of confusion over versions. Rgraphviz's current version is 1.18.1, which was build using Graphviz 2.16.1. To make matters worse, there is also a stable Graphviz 2.18 version. Jenny At 01:33 PM 6/3/2008, Tony Chiang wrote: >Sorry Jenny, > >I forgot to ask...you mention that you were using Rgraphviz_1.18.1 but then >say you installed 2.16.1, why is that? > >On Tue, Jun 3, 2008 at 7:27 PM, Tony Chiang <tchiang at="" fhcrc.org=""> wrote: > > > Hi Jenny, > > > > Someone had the same error and posted the question to the mailing list. > > Martin had a suggestion about setting the path correctly (as Li also > > mentioned). Here is Martin's reply: > > > > The Rgraphviz currently available for Windows with biocLite is built > >> with graphviz 2.16, so you'll need to install > >> > >> http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz > >> -win-2.16.1.bin.tar.gz > >> > >> Likely the problem you have below is because the path to graphviz > >> needs to be added to your system PATH variable, e.g., settings -> control > >> panels -> system -> advanced -> Environment Variables and then adding > >> or editing a variable PATH to contain the path to graphviz' bin > >> directory. My path reads in part > >> > >> C:\Program Files\Graphviz2.16\Bin > >> > >> The version of graphviz installed on your computer has to match the > >> version used to build Rgraphviz, so 2.18 will not work. > >> > >> Martin > > > > > > I use google mail, so I can search in my folders for past post fairly > > easily. There are quite a few posts about Rgraphviz, and I > understand it has > > been hard for people to get things working. I use a mac almost exclusively, > > and had a rough time with it as well. > > > > But searching the archives and (if there is no reasonable answers there) > > letting us know what went wrong will let us better help. > > > > cheers, > > --tony > > > > On Tue, Jun 3, 2008 at 7:14 PM, Jenny Drnevich <drnevich at="" illinois.edu=""> > > wrote: > > > >> Hi Tony, > >> > >> Actually, I have NOT been able to get Rgraphviz to work with R 2.7.0, and > >> I've tried two different Windows machines. I'm not sure the problem > >> completely lies with Rgraphviz, but maybe with Graphviz as well. > Even though > >> I want to use the Rgraphviz Windows binary instead of building > Rgraphviz, I > >> followed the README file found in the Rgraphviz_1.18.1.tar.gz source file: > >> > >> 1. I'm not sure how to "make sure your MSVCR80.DLL is from Microsoft > >> Visual C++ 2005 SP1 Redistributable Package", but I downloaded > and installed > >> the package from the link provided, following all their instructions and > >> warnings. > >> > >> 2. I downloaded and installed the graphviz-2.16.1.static.exe binary from > >> Graphviz.org, which is the only 2.16 version available. > >> > >> 3. I created the new user variables as indicated, and made sure the > >> C:\Program Files\graphviz-2.16\bin was added to my path (it was done > >> automatically) > >> > >> 4. Then I used biocLite() to install Rgraphviz. > >> > >> When I tried to load Rgraphviz, I got both a Windows error and an error > >> within R; The Windows error message is known to Graphviz because it is > >> mentioned on the download page: "The application has failed to > start because > >> somefilename.dll was not found. Re-installing the application may fix this > >> problem." Graphviz says to install Microsoft Visual C++ 2005 > >> Redistributable Package (x86) to fix it, but I've already done that! > >> > >> The R error message is: > >> > library(Rgraphviz) > >> Loading required package: grid > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library > >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > >> Error: package/namespace load failed for 'Rgraphviz' > >> > >> > >> Finally, I finished the directions in the README file to safely load > >> Rgraphviz but I got another error message: > >> > >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library 'C:/Program > >> Files/graphviz-2.16/bin/gvc.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz > >> from source have created it? I'm still having the general Windows problem > >> related to the Microsoft Visual C++ 2005 Redistributable Package (x86), > >> which I have no idea how to fix. I'd be very interested in > hearing if anyone > >> has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 > and how they > >> did it. If someone knows what I'm doing wrong or have other suggestions to > >> try, please let me now! Overall, I doubt that a generic/novice Windows R > >> user could be able to get Rgraphviz to work... > >> > >> Thanks, > >> Jenny > >> > >> > sessionInfo() > >> R version 2.7.0 (2008-04-22) > >> i386-pc-mingw32 > >> > >> locale: > >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > >> States.1252;LC_MONETARY=English_United > >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >> > >> attached base packages: > >> [1] grid splines tools stats graphics grDevices utils > >> [8] datasets methods base > >> > >> other attached packages: > >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 > >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 > >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 > >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 > >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 > >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 > >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 > >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 > >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 > >> > >> loaded via a namespace (and not attached): > >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > >> > >> > > >> > >> > >> > >> > >> At 10:39 AM 6/3/2008, Tony Chiang wrote: > >> > >>> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who > >>> have gotten Rgraphviz to work. Unless you let us who what seems to be the > >>> problem on your end, I would suggest reading the large number of e-mails > >>> from the archives that deals with the different issues that have come > >>> up...and maybe it might solve your problems. > >>> > >>> tony > >>> > >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at="" email.unc.edu=""> > >>> wrote: > >>> > >>> > Hello all, > >>> > > >>> > I'm creating an application which use rJava to connect with R. But my > >>> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in > >>> nearest > >>> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean > >>> that > >>> > for installing Rgraphviz I need just run these two strings in R: > >>> > > >>> > /source("http://bioconductor.org/biocLite.R") > >>> > biocLite("Rgraphviz") > >>> > > >>> > /?/ > >>> > / > >>> > > >>> > -- > >>> > Best regards, Myroslav > >>> > > >>> > _______________________________________________ > >>> > Bioconductor mailing list > >>> > Bioconductor at stat.math.ethz.ch > >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > Search the archives: > >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > >> Jenny Drnevich, Ph.D. > >> > >> Functional Genomics Bioinformatics Specialist > >> W.M. Keck Center for Comparative and Functional Genomics > >> Roy J. Carver Biotechnology Center > >> University of Illinois, Urbana-Champaign > >> > >> 330 ERML > >> 1201 W. Gregory Dr. > >> Urbana, IL 61801 > >> USA > >> > >> ph: 217-244-7355 > >> fax: 217-265-5066 > >> e-mail: drnevich at illinois.edu > >> > > > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
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Jenny Drnevich ★ 2.0k
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> > > Actually, you don't want this static version. Instead go looking here > > > > http://www.graphviz.org/pub/graphviz/ARCHIVE/ > > > > Make sure to clean up as completely as possible your previous installation. > > > > I *think*, contrary to previous posts of mine, that you can also use the > > recent graphviz (2.18), so long as you're building Rgraphviz yourself. > > > >At least on my Macbook pro, this is true (at least it works for me without >failing). Jenny, if >you use biocLite, make sure that you set the type="source" to build it from >source. Using the archived Graphviz 2.16 didn't change anything - still same errors. Also, I'm deliberately not building Rgraphviz from source, but instead trying to get the Windows binary to work. If it can't be made to work, perhaps the Windows binary should be removed? Thanks, Jenny > > > > Once built, your Rgraphviz will still have missing functionality, in > > particular it will be unable to read / write graph objects using agopen, > > agwrite, etc. This seems to be a complex issue in the interaction between R > > and graphviz, tracing I think to the use of different development tools for > > the two project. There might be similar surprises in other functions; these > > are just the ones that the Bioc build machine stumbles on when checking the > > package. You'll encounter missing functionality in a most unpleasant way, > > abruptly aborting your session. > > > >I don't have access to a windows machine at the moment, but this also >happened on my mac a few months back (always with the agopen and agwrite). >After I grab the lastest X-code (with the latest compliers) and built both >graphviz and Rgraphviz from source on the (also following Martin's advice to >make sure that all previous incarnations of graphviz were completely removed >before building graphviz again), this problem seems to have gone away. > > > > > > I think the rationale for not updating the instructions in the package, or > > making some functionality 'optional' on windows, is the hope for a more > > robust solution. > > > > Again I seem to have a poor track record on providing reliable information > > about this, so please take with a grain of salt. > > > >I should say ditto for me too now! > > > > > > Martin > > > > > > 3. I created the new user variables as indicated, and made sure the > >> C:\Program Files\graphviz-2.16\bin was added to my path (it was done > >> automatically) > >> > >> 4. Then I used biocLite() to install Rgraphviz. > >> > >> When I tried to load Rgraphviz, I got both a Windows error and an error > >> within R; The Windows error message is known to Graphviz because it is > >> mentioned on the download page: "The application has failed to > start because > >> somefilename.dll was not found. Re-installing the application may fix this > >> problem." Graphviz says to install Microsoft Visual C++ 2005 > >> Redistributable Package (x86) to fix it, but I've already done that! > >> > >> The R error message is: > >> > library(Rgraphviz) > >> Loading required package: grid > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library > >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > >> Error: package/namespace load failed for 'Rgraphviz' > >> > >> > >> Finally, I finished the directions in the README file to safely load > >> Rgraphviz but I got another error message: > >> > >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library 'C:/Program > >> Files/graphviz-2.16/bin/gvc.dll': > >> LoadLibrary failure: The specified module could not be found. > >> > >> > >> So is this gvc.dll file missing from Graphviz? Or would building Rgraphviz > >> from source have created it? I'm still having the general Windows problem > >> related to the Microsoft Visual C++ 2005 Redistributable Package (x86), > >> which I have no idea how to fix. I'd be very interested in > hearing if anyone > >> has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 > and how they > >> did it. If someone knows what I'm doing wrong or have other suggestions to > >> try, please let me now! Overall, I doubt that a generic/novice Windows R > >> user could be able to get Rgraphviz to work... > >> > >> Thanks, > >> Jenny > >> > >> > sessionInfo() > >> R version 2.7.0 (2008-04-22) > >> i386-pc-mingw32 > >> > >> locale: > >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > >> States.1252;LC_MONETARY=English_United > >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >> > >> attached base packages: > >> [1] grid splines tools stats graphics grDevices utils > >> [8] datasets methods base > >> > >> other attached packages: > >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 > >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 > >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 > >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 > >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 > >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 > >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 > >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 > >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 > >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 > >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 > >> > >> loaded via a namespace (and not attached): > >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 > >> > > >> > >> > >> > >> > >> At 10:39 AM 6/3/2008, Tony Chiang wrote: > >> > >>> I am sure that there are plenty of folks with Windows XP and R-2.7.0 who > >>> have gotten Rgraphviz to work. Unless you let us who what seems to be the > >>> problem on your end, I would suggest reading the large number of e-mails > >>> from the archives that deals with the different issues that have come > >>> up...and maybe it might solve your problems. > >>> > >>> tony > >>> > >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at="" email.unc.edu=""> > >>> wrote: > >>> > >>> > Hello all, > >>> > > >>> > I'm creating an application which use rJava to connect with R. But my > >>> > question is about Rgraphviz. Could you tell me if Rgraphviz will (in > >>> nearest > >>> > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean > >>> that > >>> > for installing Rgraphviz I need just run these two strings in R: > >>> > > >>> > /source("http://bioconductor.org/biocLite.R") > >>> > biocLite("Rgraphviz") > >>> > > >>> > /?/ > >>> > / > >>> > > >>> > -- > >>> > Best regards, Myroslav > >>> > > >>> > _______________________________________________ > >>> > Bioconductor mailing list > >>> > Bioconductor at stat.math.ethz.ch > >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > Search the archives: > >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > >> Jenny Drnevich, Ph.D. > >> > >> Functional Genomics Bioinformatics Specialist > >> W.M. Keck Center for Comparative and Functional Genomics > >> Roy J. Carver Biotechnology Center > >> University of Illinois, Urbana-Champaign > >> > >> 330 ERML > >> 1201 W. Gregory Dr. > >> Urbana, IL 61801 > >> USA > >> > >> ph: 217-244-7355 > >> fax: 217-265-5066 > >> e-mail: drnevich at illinois.edu > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > -- > > Martin Morgan > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M2 B169 > > Phone: (206) 667-2793 > > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
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Jenny Drnevich wrote: > >> >> > Actually, you don't want this static version. Instead go looking here >> > >> > http://www.graphviz.org/pub/graphviz/ARCHIVE/ >> > >> > Make sure to clean up as completely as possible your previous >> installation. >> > >> > I *think*, contrary to previous posts of mine, that you can also use >> the >> > recent graphviz (2.18), so long as you're building Rgraphviz yourself. >> > >> >> At least on my Macbook pro, this is true (at least it works for me >> without >> failing). Jenny, if >> you use biocLite, make sure that you set the type="source" to build it >> from >> source. > > Using the archived Graphviz 2.16 didn't change anything - still same > errors. Also, I'm deliberately not building Rgraphviz from source, but > instead trying to get the Windows binary to work. If it can't be made to > work, perhaps the Windows binary should be removed? In the short - and likely even medium term that may be the only solution. There do not seem to be easy ways to build a DLL that is compliant (which is why the very old one was retained for such a long time) and it requires a substantial effort with every new version of Graphviz that comes out - given competing needs for scarce resources, I am afraid that this is likely to be a month or more. best wishes Robert > > Thanks, > Jenny > > > > > >> > >> > Once built, your Rgraphviz will still have missing functionality, in >> > particular it will be unable to read / write graph objects using >> agopen, >> > agwrite, etc. This seems to be a complex issue in the interaction >> between R >> > and graphviz, tracing I think to the use of different development >> tools for >> > the two project. There might be similar surprises in other >> functions; these >> > are just the ones that the Bioc build machine stumbles on when >> checking the >> > package. You'll encounter missing functionality in a most unpleasant >> way, >> > abruptly aborting your session. >> > >> >> I don't have access to a windows machine at the moment, but this also >> happened on my mac a few months back (always with the agopen and >> agwrite). >> After I grab the lastest X-code (with the latest compliers) and built >> both >> graphviz and Rgraphviz from source on the (also following Martin's >> advice to >> make sure that all previous incarnations of graphviz were completely >> removed >> before building graphviz again), this problem seems to have gone away. >> >> >> > >> > I think the rationale for not updating the instructions in the >> package, or >> > making some functionality 'optional' on windows, is the hope for a more >> > robust solution. >> > >> > Again I seem to have a poor track record on providing reliable >> information >> > about this, so please take with a grain of salt. >> > >> >> I should say ditto for me too now! >> >> >> > >> > Martin >> > >> > >> > 3. I created the new user variables as indicated, and made sure the >> >> C:\Program Files\graphviz-2.16\bin was added to my path (it was done >> >> automatically) >> >> >> >> 4. Then I used biocLite() to install Rgraphviz. >> >> >> >> When I tried to load Rgraphviz, I got both a Windows error and an >> error >> >> within R; The Windows error message is known to Graphviz because it is >> >> mentioned on the download page: "The application has failed to >> start because >> >> somefilename.dll was not found. Re-installing the application may >> fix this >> >> problem." Graphviz says to install Microsoft Visual C++ 2005 >> >> Redistributable Package (x86) to fix it, but I've already done that! >> >> >> >> The R error message is: >> >> > library(Rgraphviz) >> >> Loading required package: grid >> >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> >> unable to load shared library >> >> 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': >> >> LoadLibrary failure: The specified module could not be found. >> >> >> >> >> >> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' >> >> Error: package/namespace load failed for 'Rgraphviz' >> >> >> >> >> >> Finally, I finished the directions in the README file to safely load >> >> Rgraphviz but I got another error message: >> >> >> >> > dyn.load("C:/Program Files/graphviz-2.16/bin/gvc.dll") >> >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> >> unable to load shared library 'C:/Program >> >> Files/graphviz-2.16/bin/gvc.dll': >> >> LoadLibrary failure: The specified module could not be found. >> >> >> >> >> >> So is this gvc.dll file missing from Graphviz? Or would building >> Rgraphviz >> >> from source have created it? I'm still having the general Windows >> problem >> >> related to the Microsoft Visual C++ 2005 Redistributable Package >> (x86), >> >> which I have no idea how to fix. I'd be very interested in hearing >> if anyone >> >> has gotten the Rgraphviz Windows _binary_ working with R 2.7.0 and >> how they >> >> did it. If someone knows what I'm doing wrong or have other >> suggestions to >> >> try, please let me now! Overall, I doubt that a generic/novice >> Windows R >> >> user could be able to get Rgraphviz to work... >> >> >> >> Thanks, >> >> Jenny >> >> >> >> > sessionInfo() >> >> R version 2.7.0 (2008-04-22) >> >> i386-pc-mingw32 >> >> >> >> locale: >> >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> >> States.1252;LC_MONETARY=English_United >> >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> >> >> attached base packages: >> >> [1] grid splines tools stats graphics grDevices utils >> >> [8] datasets methods base >> >> >> >> other attached packages: >> >> [1] affyQCReport_1.18.0 geneplotter_1.18.0 lattice_0.17-8 >> >> [4] RColorBrewer_1.0-2 simpleaffy_2.16.0 made4_1.14.0 >> >> [7] ade4_1.4-7 affyPLM_1.16.0 affycoretools_1.12.0 >> >> [10] annaffy_1.12.0 KEGG.db_2.2.0 gcrma_2.12.0 >> >> [13] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.8-1 >> >> [16] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 >> >> [19] survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 >> >> [22] xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.0 >> >> [25] RSQLite_0.6-8 DBI_0.2-4 graph_1.18.1 >> >> [28] limma_2.14.1 affy_1.18.0 preprocessCore_1.2.0 >> >> [31] affyio_1.8.0 Biobase_2.0.1 RWinEdt_1.8-0 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] cluster_1.11.10 KernSmooth_2.22-22 XML_1.94-0.1 >> >> > >> >> >> >> >> >> >> >> >> >> At 10:39 AM 6/3/2008, Tony Chiang wrote: >> >> >> >>> I am sure that there are plenty of folks with Windows XP and >> R-2.7.0 who >> >>> have gotten Rgraphviz to work. Unless you let us who what seems to >> be the >> >>> problem on your end, I would suggest reading the large number of >> e-mails >> >>> from the archives that deals with the different issues that have come >> >>> up...and maybe it might solve your problems. >> >>> >> >>> tony >> >>> >> >>> On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa at="" email.unc.edu=""> >> >>> wrote: >> >>> >> >>> > Hello all, >> >>> > >> >>> > I'm creating an application which use rJava to connect with R. >> But my >> >>> > question is about Rgraphviz. Could you tell me if Rgraphviz will >> (in >> >>> nearest >> >>> > future) work with R 2.7.0 as it has been working with R 2.6.*? I >> mean >> >>> that >> >>> > for installing Rgraphviz I need just run these two strings in R: >> >>> > >> >>> > /source("http://bioconductor.org/biocLite.R") >> >>> > biocLite("Rgraphviz") >> >>> > >> >>> > /?/ >> >>> > / >> >>> > >> >>> > -- >> >>> > Best regards, Myroslav >> >>> > >> >>> > _______________________________________________ >> >>> > Bioconductor mailing list >> >>> > Bioconductor at stat.math.ethz.ch >> >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>> > Search the archives: >> >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>> > >> >>> >> >>> [[alternative HTML version deleted]] >> >>> >> >>> _______________________________________________ >> >>> Bioconductor mailing list >> >>> Bioconductor at stat.math.ethz.ch >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>> Search the archives: >> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>> >> >> >> >> Jenny Drnevich, Ph.D. >> >> >> >> Functional Genomics Bioinformatics Specialist >> >> W.M. Keck Center for Comparative and Functional Genomics >> >> Roy J. Carver Biotechnology Center >> >> University of Illinois, Urbana-Champaign >> >> >> >> 330 ERML >> >> 1201 W. Gregory Dr. >> >> Urbana, IL 61801 >> >> USA >> >> >> >> ph: 217-244-7355 >> >> fax: 217-265-5066 >> >> e-mail: drnevich at illinois.edu >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at stat.math.ethz.ch >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > >> > >> > -- >> > Martin Morgan >> > Computational Biology / Fred Hutchinson Cancer Research Center >> > 1100 Fairview Ave. N. >> > PO Box 19024 Seattle, WA 98109 >> > >> > Location: Arnold Building M2 B169 >> > Phone: (206) 667-2793 >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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> > In the short - and likely even medium term that may be the only > solution. There do not seem to be easy ways to build a DLL that is > compliant (which is why the very old one was retained for such a long > time) and it requires a substantial effort with every new version of > Graphviz that comes out - given competing needs for scarce resources, I > am afraid that this is likely to be a month or more. > > best wishes > Robert > Hi, Graphviz releases are also not as stable as one would hope: (1) graphviz 2.16 didn't contain some required .dlls as graphviz 2.15, which causes a lot of confusions, it seems like graphviz 2.18 contains all the .dlls needed and it works ok in linking; the README was written when testing was done for graphviz 2.15, assuming graphviz releases are somewhat stable... (2) graphviz built on Windows uses Microsoft Visual Studio, not minGW or any thing Linux-like, and the developers strongly discourage build-your-own approach; when mixing the .obj from these different sources, things are pretty nasty, and we (me and graphviz developers) haven't found a way out; it seems that the suggestion from graphviz users and developers is to use .dlls; It's not without trying... Li
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Tony Chiang ▴ 570
@tony-chiang-1769
Last seen 10.2 years ago
I am sure that there are plenty of folks with Windows XP and R-2.7.0 who have gotten Rgraphviz to work. Unless you let us who what seems to be the problem on your end, I would suggest reading the large number of e-mails from the archives that deals with the different issues that have come up...and maybe it might solve your problems. tony On Tue, Jun 3, 2008 at 4:09 PM, Myroslav Sypa <msypa@email.unc.edu> wrote: > Hello all, > > I'm creating an application which use rJava to connect with R. But my > question is about Rgraphviz. Could you tell me if Rgraphviz will (in nearest > future) work with R 2.7.0 as it has been working with R 2.6.*? I mean that > for installing Rgraphviz I need just run these two strings in R: > > /source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") > > /?/ > / > > -- > Best regards, Myroslav > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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@lilongisb-sibch-1725
Last seen 10.2 years ago
Hi, There are some major changes in Rgraphviz on Windows from BioC 2.6 to 2.7, mainly to support various versions of graphviz. Before BioC 2.6, Rgraphviz on Windows uses VERY OLD graphviz (more than 2 year old) only. Since BioC 2.7, Rgraphviz on Windows is parallel to that on Linux, i.e., you can use different version of graphviz on Windows. The downside of this is that you have to install graphviz on Windows and set up a few env variables before install Rgraphviz. Back to the question: (1) yes, Rgraphviz works with BioC 2.7, (2) no, Rgraphviz works with BioC 2.7 in a different way as with BioC 2.6. If you don't install graphviz on Windows for various reasons, I think you can retrieve older version of Rgraphviz and it should work with BioC 2.6. Hope this helps. Li > Hello all, > > I'm creating an application which use rJava to connect with R. But my > question is about Rgraphviz. Could you tell me if Rgraphviz will (in > nearest future) work with R 2.7.0 as it has been working with R 2.6.*? I > mean that for installing Rgraphviz I need just run these two strings in R: > > /source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") > > /?/ > / > > -- > Best regards, Myroslav > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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