problems loading the Rgraphviz package
1
0
Entering edit mode
li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 6.5 years ago
I have problems loading the Rgraphviz package under Windows with the newest version of R. I installed Rgraphviz package using biocLite("Rgraphviz") method and the package version of Rgraphviz is 1.18.0.(Also, I have installed the "Rgraphviz" version 1.16.0 with no trouble at all) Here is the error message I am getting: ---- Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.0RC/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' ----- The version of Bioconductor is 2.2. And here is the session info: ############ R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Chinese_People's Republic of China.936;LC_CTYPE=Chinese_People's Republic of China.936;LC_MONETARY=Chinese_People's Republic of China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] graph_1.18.0 loaded via a namespace (and not attached): [1] cluster_1.11.10 tools_2.7.0 ############ Thanks! --- LiGang [[alternative HTML version deleted]]
Rgraphviz Rgraphviz • 2.1k views
ADD COMMENT •
0
Entering edit mode
@martin-morgan-1513
Last seen 4 months ago
United States
Hi -- 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 LiGang <luzifer.li at="" gmail.com=""> writes: > I have problems loading the Rgraphviz package under Windows with the newest > version of R. > > I installed Rgraphviz package using biocLite("Rgraphviz") method and the > package version of Rgraphviz is 1.18.0.(Also, I have installed the > "Rgraphviz" version 1.16.0 with no trouble at all) > > > > Here is the error message I am getting: > > ---- > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.0RC/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' > ----- > > The version of Bioconductor is 2.2. > > And here is the session info: > ############ > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=Chinese_People's Republic of China.936;LC_CTYPE=Chinese_People's > Republic of China.936;LC_MONETARY=Chinese_People's Republic of > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] graph_1.18.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 tools_2.7.0 > ############ > > Thanks! > > --- > LiGang > > [[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 -- 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
ADD COMMENT •
0
Entering edit mode
Hi Martin, I just ran into this problem myself, and I'm a little confused as to your response. I was looking at all the documentation/vignettes for Rgraphviz, and it's not very clear or explicit either. First of all, there is very little mention of needing graphviz in Rgraphviz; In Details it does say SystemRequirements - Graphviz version >= 2.2 , but that's all. It would be useful if in one or both of the vignettes at the beginning there was a description that an external program was needed, and where to go to download it. The only mention of it all in either vignette is at the end in the SessionInfo section, which has hard-coded "together with version 2.12 of graphviz." My other confusion is what version of graphviz is needed. The SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes is obviously wrong and a hold-over from the previous version. You say below Rgraphviz is built with graphviz 2.16. However, the graphviz website (http://www.graphviz.org/Download_windows.php) shows two stable versions, 2.16.1.static and 2.18. The SystemRequirements is obviously wrong since the developmental version is only 2.19. And I wasn't sure what you were referring to below when you said >The version of graphviz installed on your computer has to match the >version used to build Rgraphviz, so 2.18 will not work. I assume the 2.18 is referring to the graphviz 2.18 and not a typo of Rgraphviz 1.18? There wasn't any mention of a higher version of graphviz in your e-mail, but now it makes since after visiting the graphviz website and noticing the ARCHIVE in the link you posted. So I guess that after all, I need to have graphviz 2.16 installed (AND in my path - another point for the vignette) ? I just wanted to point out that this information is apparently not associated with Rgraphviz at all, except for this post, and will likely cause other users problems. Oh, and I just noticed this Note to Windows users on the graphviz page: Meanwhile, if you get error messages like: "The application has failed to start because somefilename.dll was not found. Re-installing the application may fix this problem." please click this <http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en">link and install Microsoft Visual C++ 2005 Redistributable Package (x86). I had that problem as well. Good to see how to fix it. Overall, a VERY difficult packages for (windows) users to get running. Thanks, Jenny At 08:02 AM 5/8/2008, Martin Morgan wrote: >Hi -- > >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 > > >LiGang <luzifer.li@gmail.com> writes: > > > I have problems loading the Rgraphviz package under Windows > with the newest > > version of R. > > > > I installed Rgraphviz package using biocLite("Rgraphviz") method and the > > package version of Rgraphviz is 1.18.0.(Also, I have installed the > > "Rgraphviz" version 1.16.0 with no trouble at all) > > > > > > > > Here is the error message I am getting: > > > > ---- > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > > unable to load shared library > > 'C:/PROGRA~1/R/R-27~1.0RC/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' > > ----- > > > > The version of Bioconductor is 2.2. > > > > And here is the session info: > > ############ > > R version 2.7.0 (2008-04-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=Chinese_People's Republic of China.936;LC_CTYPE=Chinese_People's > > Republic of China.936;LC_MONETARY=Chinese_People's Republic of > > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] graph_1.18.0 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.10 tools_2.7.0 > > ############ > > > > Thanks! > > > > --- > > LiGang > > > > [[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 > >-- >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 > >_______________________________________________ >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@uiuc.edu [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
This problem is really only for people using Graphviz on Windows using a binary version. If you compile Rgraphviz (say on Linux or Mac OS X) you just install whatever version of graphviz you need and then compile against it. The problem is really for Windows users using the BINARY version of the RGraphviz package (which most people do I think). You then need the exact same binary version of Graphviz as was used to create the RGraphviz binary version. This is apparently 2.16. Let me iterate: the graphviz >= 12 is only really for people compiling from source. Now, this is a major change from earlier where Graphviz 2.2 was included with the RGraphviz package for Windows users. This was great - no-one had to do anything to get it going. Unfortunately that package is beginning to get outdated and it is (for various reasons) very difficult to do that trick again. So someone decided to make people install the binary version of Graphviz 2.16 for Windows users. I agree with Jenny that this is a major change and it should be kind of highlighted. The fact that she has missed this information is probably an indication that something need to be added somewhere. My guess is that this was overlooked? Especially since it is a very specific version of graphviz requested and not just any >= 2.12. Kasper On May 8, 2008, at 11:50 AM, Jenny Drnevich wrote: > Hi Martin, > > I just ran into this problem myself, and I'm a little confused as to > your response. I was looking at all the documentation/vignettes for > Rgraphviz, and it's not very clear or explicit either. First of all, > there is very little mention of needing graphviz in Rgraphviz; In > Details it does say SystemRequirements - Graphviz version >= 2.2 , > but that's all. It would be useful if in one or both of the vignettes > at the beginning there was a description that an external program was > needed, and where to go to download it. The only mention of it all in > either vignette is at the end in the SessionInfo section, which has > hard-coded "together with version 2.12 of graphviz." > > My other confusion is what version of graphviz is needed. The > SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes > is obviously wrong and a hold-over from the previous version. You say > below Rgraphviz is built with graphviz 2.16. However, the graphviz > website (http://www.graphviz.org/Download_windows.php) shows two > stable versions, 2.16.1.static and 2.18. The SystemRequirements is > obviously wrong since the developmental version is only 2.19. And I > wasn't sure what you were referring to below when you said > >> The version of graphviz installed on your computer has to match the >> version used to build Rgraphviz, so 2.18 will not work. > > I assume the 2.18 is referring to the graphviz 2.18 and not a typo of > Rgraphviz 1.18? There wasn't any mention of a higher version of > graphviz in your e-mail, but now it makes since after visiting the > graphviz website and noticing the ARCHIVE in the link you posted. So > I guess that after all, I need to have graphviz 2.16 installed (AND > in my path - another point for the vignette) ? I just wanted to > point out that this information is apparently not associated with > Rgraphviz at all, except for this post, and will likely cause other > users problems. > > Oh, and I just noticed this Note to Windows users on the graphviz > page: > > Meanwhile, if you get error messages like: > "The application has failed to start because somefilename.dll was not > found. Re-installing the application may fix this problem." > please click this > <http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en"> >link > and install Microsoft Visual C++ 2005 Redistributable Package (x86). > > I had that problem as well. Good to see how to fix it. Overall, a > VERY difficult packages for (windows) users to get running. > > > Thanks, > Jenny > > At 08:02 AM 5/8/2008, Martin Morgan wrote: >> Hi -- >> >> 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 >> >> >> LiGang <luzifer.li at="" gmail.com=""> writes: >> >>> I have problems loading the Rgraphviz package under Windows >> with the newest >>> version of R. >>> >>> I installed Rgraphviz package using biocLite("Rgraphviz") method >>> and the >>> package version of Rgraphviz is 1.18.0.(Also, I have installed the >>> "Rgraphviz" version 1.16.0 with no trouble at all) >>> >>> >>> >>> Here is the error message I am getting: >>> >>> ---- >>> Error in inDL(x, as.logical(local), as.logical(now), ...) : >>> unable to load shared library >>> 'C:/PROGRA~1/R/R-27~1.0RC/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' >>> ----- >>> >>> The version of Bioconductor is 2.2. >>> >>> And here is the session info: >>> ############ >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=Chinese_People's Republic of China. >>> 936;LC_CTYPE=Chinese_People's >>> Republic of China.936;LC_MONETARY=Chinese_People's Republic of >>> China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China. >>> 936 >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets >>> methods >>> base >>> >>> other attached packages: >>> [1] graph_1.18.0 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.10 tools_2.7.0 >>> ############ >>> >>> Thanks! >>> >>> --- >>> LiGang >>> >>> [[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 >> >> -- >> 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 >> >> _______________________________________________ >> 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 uiuc.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
ADD REPLY •
0
Entering edit mode
Well, that is not exactly true... On Thu, May 8, 2008 at 8:26 PM, Kasper Daniel Hansen < khansen@stat.berkeley.edu> wrote: > This problem is really only for people using Graphviz on Windows using a > binary version. > > If you compile Rgraphviz (say on Linux or Mac OS X) you just install > whatever version of graphviz you need and then compile against it. > You are correct if someone is going to build Rgraphviz from source, but there are people who do use Max OS X as well as some Linux users who do just download the binary files. In general, I have work exclusively on a Mac with Tiger, and I usually download the binary stable version of R from Simon's homepage while I always build the development version of R from source. This time around, I had to compile Rgraphviz locally for both R and R-devel to get anything to work. This is after upgrading all the compilers, gcc, graphviz, etc. I don't know if this is what is meant for the general user's of R. Most people who use R where I work would not be able to do all this (some could and would). > > The problem is really for Windows users using the BINARY version of the > RGraphviz package (which most people do I think). You then need the exact > same binary version of Graphviz as was used to create the RGraphviz binary > version. This is apparently 2.16. > > Let me iterate: the graphviz >= 12 is only really for people compiling from > source. > > Now, this is a major change from earlier where Graphviz 2.2 was included > with the RGraphviz package for Windows users. This was great - no- one had to > do anything to get it going. Unfortunately that package is beginning to get > outdated and it is (for various reasons) very difficult to do that trick > again. > > So someone decided to make people install the binary version of Graphviz > 2.16 for Windows users. I agree with Jenny that this is a major change and > it should be kind of highlighted. The fact that she has missed this > information is probably an indication that something need to be added > somewhere. My guess is that this was overlooked? Especially since it is a > very specific version of graphviz requested and not just any >= 2.12. > > Kasper > > > On May 8, 2008, at 11:50 AM, Jenny Drnevich wrote: > > Hi Martin, >> >> I just ran into this problem myself, and I'm a little confused as to >> your response. I was looking at all the documentation/vignettes for >> Rgraphviz, and it's not very clear or explicit either. First of all, >> there is very little mention of needing graphviz in Rgraphviz; In >> Details it does say SystemRequirements - Graphviz version >= 2.2 , >> but that's all. It would be useful if in one or both of the vignettes >> at the beginning there was a description that an external program was >> needed, and where to go to download it. The only mention of it all in >> either vignette is at the end in the SessionInfo section, which has >> hard-coded "together with version 2.12 of graphviz." >> >> My other confusion is what version of graphviz is needed. The >> SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes >> is obviously wrong and a hold-over from the previous version. You say >> below Rgraphviz is built with graphviz 2.16. However, the graphviz >> website (http://www.graphviz.org/Download_windows.php) shows two >> stable versions, 2.16.1.static and 2.18. The SystemRequirements is >> obviously wrong since the developmental version is only 2.19. And I >> wasn't sure what you were referring to below when you said >> >> The version of graphviz installed on your computer has to match the >>> version used to build Rgraphviz, so 2.18 will not work. >>> >> >> I assume the 2.18 is referring to the graphviz 2.18 and not a typo of >> Rgraphviz 1.18? There wasn't any mention of a higher version of >> graphviz in your e-mail, but now it makes since after visiting the >> graphviz website and noticing the ARCHIVE in the link you posted. So >> I guess that after all, I need to have graphviz 2.16 installed (AND >> in my path - another point for the vignette) ? I just wanted to >> point out that this information is apparently not associated with >> Rgraphviz at all, except for this post, and will likely cause other >> users problems. >> >> Oh, and I just noticed this Note to Windows users on the graphviz page: >> >> Meanwhile, if you get error messages like: >> "The application has failed to start because somefilename.dll was not >> found. Re-installing the application may fix this problem." >> please click this >> < >> http://www.microsoft.com/downloads/details.aspx?familyid=32bc1bee- a3f9-4c13-9c99-220b62a191ee&displaylang=en >> >link >> and install Microsoft Visual C++ 2005 Redistributable Package (x86). >> >> I had that problem as well. Good to see how to fix it. Overall, a >> VERY difficult packages for (windows) users to get running. >> >> >> Thanks, >> Jenny >> >> At 08:02 AM 5/8/2008, Martin Morgan wrote: >> >>> Hi -- >>> >>> 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 >>> >>> >>> LiGang <luzifer.li@gmail.com> writes: >>> >>> I have problems loading the Rgraphviz package under Windows >>>> >>> with the newest >>> >>>> version of R. >>>> >>>> I installed Rgraphviz package using biocLite("Rgraphviz") method and the >>>> package version of Rgraphviz is 1.18.0.(Also, I have installed the >>>> "Rgraphviz" version 1.16.0 with no trouble at all) >>>> >>>> >>>> >>>> Here is the error message I am getting: >>>> >>>> ---- >>>> Error in inDL(x, as.logical(local), as.logical(now), ...) : >>>> unable to load shared library >>>> 'C:/PROGRA~1/R/R-27~1.0RC/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' >>>> ----- >>>> >>>> The version of Bioconductor is 2.2. >>>> >>>> And here is the session info: >>>> ############ >>>> R version 2.7.0 (2008-04-22) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=Chinese_People's Republic of >>>> China.936;LC_CTYPE=Chinese_People's >>>> Republic of China.936;LC_MONETARY=Chinese_People's Republic of >>>> China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 >>>> >>>> attached base packages: >>>> [1] grid stats graphics grDevices utils datasets methods >>>> base >>>> >>>> other attached packages: >>>> [1] graph_1.18.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] cluster_1.11.10 tools_2.7.0 >>>> ############ >>>> >>>> Thanks! >>>> >>>> --- >>>> LiGang >>>> >>>> [[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 >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> 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@uiuc.edu >> [[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 >> > > _______________________________________________ > 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]]
ADD REPLY •
0
Entering edit mode
On May 8, 2008, at 12:44 PM, Tony Chiang wrote: > Well, that is not exactly true... > > On Thu, May 8, 2008 at 8:26 PM, Kasper Daniel Hansen <khansen@stat.berkeley.edu> > wrote: > This problem is really only for people using Graphviz on Windows > using a binary version. > > If you compile Rgraphviz (say on Linux or Mac OS X) you just install > whatever version of graphviz you need and then compile against it. > > You are correct if someone is going to build Rgraphviz from source, > but there are people who do use Max OS X as well as some Linux users > who do just download the binary files. > > In general, I have work exclusively on a Mac with Tiger, and I > usually download the binary stable version of R from Simon's > homepage while I always build the development version of R from > source. This time around, I had to compile Rgraphviz locally for > both R and R-devel to get anything to work. This is after upgrading > all the compilers, gcc, graphviz, etc. > > I don't know if this is what is meant for the general user's of R. > Most people who use R where I work would not be able to do all this > (some could and would). In case my position was unclear: I totally agree with you on this one: Rgraphviz has been made much more difficult to install on Windows. Possibly also on OS X, although I haven't checked (your comment seems to indicate it though). On Linux I would have to disagree: no-one (as far as I know) provides binaries for Linux. And these changes have happened without much fanfare. Kasper > > > The problem is really for Windows users using the BINARY version of > the RGraphviz package (which most people do I think). You then need > the exact same binary version of Graphviz as was used to create the > RGraphviz binary version. This is apparently 2.16. > > Let me iterate: the graphviz >= 12 is only really for people > compiling from source. > > Now, this is a major change from earlier where Graphviz 2.2 was > included with the RGraphviz package for Windows users. This was > great - no-one had to do anything to get it going. Unfortunately > that package is beginning to get outdated and it is (for various > reasons) very difficult to do that trick again. > > So someone decided to make people install the binary version of > Graphviz 2.16 for Windows users. I agree with Jenny that this is a > major change and it should be kind of highlighted. The fact that she > has missed this information is probably an indication that something > need to be added somewhere. My guess is that this was overlooked? > Especially since it is a very specific version of graphviz requested > and not just any >= 2.12. > > Kasper > > > On May 8, 2008, at 11:50 AM, Jenny Drnevich wrote: > > Hi Martin, > > I just ran into this problem myself, and I'm a little confused as to > your response. I was looking at all the documentation/vignettes for > Rgraphviz, and it's not very clear or explicit either. First of all, > there is very little mention of needing graphviz in Rgraphviz; In > Details it does say SystemRequirements - Graphviz version >= 2.2 , > but that's all. It would be useful if in one or both of the vignettes > at the beginning there was a description that an external program was > needed, and where to go to download it. The only mention of it all in > either vignette is at the end in the SessionInfo section, which has > hard-coded "together with version 2.12 of graphviz." > > My other confusion is what version of graphviz is needed. The > SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes > is obviously wrong and a hold-over from the previous version. You say > below Rgraphviz is built with graphviz 2.16. However, the graphviz > website (http://www.graphviz.org/Download_windows.php) shows two > stable versions, 2.16.1.static and 2.18. The SystemRequirements is > obviously wrong since the developmental version is only 2.19. And I > wasn't sure what you were referring to below when you said > > The version of graphviz installed on your computer has to match the > version used to build Rgraphviz, so 2.18 will not work. > > I assume the 2.18 is referring to the graphviz 2.18 and not a typo of > Rgraphviz 1.18? There wasn't any mention of a higher version of > graphviz in your e-mail, but now it makes since after visiting the > graphviz website and noticing the ARCHIVE in the link you posted. So > I guess that after all, I need to have graphviz 2.16 installed (AND > in my path - another point for the vignette) ? I just wanted to > point out that this information is apparently not associated with > Rgraphviz at all, except for this post, and will likely cause other > users problems. > > Oh, and I just noticed this Note to Windows users on the graphviz > page: > > Meanwhile, if you get error messages like: > "The application has failed to start because somefilename.dll was not > found. Re-installing the application may fix this problem." > please click this > <http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en"> >link > and install Microsoft Visual C++ 2005 Redistributable Package (x86). > > I had that problem as well. Good to see how to fix it. Overall, a > VERY difficult packages for (windows) users to get running. > > > Thanks, > Jenny > > At 08:02 AM 5/8/2008, Martin Morgan wrote: > Hi -- > > 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 > > > LiGang <luzifer.li@gmail.com> writes: > > I have problems loading the Rgraphviz package under Windows > with the newest > version of R. > > I installed Rgraphviz package using biocLite("Rgraphviz") method and > the > package version of Rgraphviz is 1.18.0.(Also, I have installed the > "Rgraphviz" version 1.16.0 with no trouble at all) > > > > Here is the error message I am getting: > > ---- > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library > 'C:/PROGRA~1/R/R-27~1.0RC/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' > ----- > > The version of Bioconductor is 2.2. > > And here is the session info: > ############ > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=Chinese_People's Republic of China. > 936;LC_CTYPE=Chinese_People's > Republic of China.936;LC_MONETARY=Chinese_People's Republic of > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods > base > > other attached packages: > [1] graph_1.18.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 tools_2.7.0 > ############ > > Thanks! > > --- > LiGang > > [[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 > > -- > 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 > > _______________________________________________ > 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@uiuc.edu > [[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 > > _______________________________________________ > 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]]
ADD REPLY •
0
Entering edit mode
Hi all, I'm sorry to bring this issue again, you'd think that after so much input from so many different people one would be able to install Rgraphviz without any major problems. Well, this doesn't seem to be my case... :) I have installed graphviz-2.16.1 and I have made the changes in the environment variables as indicated in the README file. The README file then says to "run "R CMD INSTALL ...Rgraphviz" as usual". I am not sure what this means. I use the RGui, so I'm guessing it might be a command that is usually run in the command prompt? In an earlier e-mail series Martin suggested that it would be possible to, after installing graphviz and make the environment variables adjustments, install Rgraphviz using biocLite. When I try doing that I get the following error: > source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor. Warning message: package 'Rgraphviz' is not available > Should this be working? Am I doing something wrong? Thanks a lot! Artur On Thu, May 8, 2008 at 4:29 PM, Kasper Daniel Hansen < khansen@stat.berkeley.edu> wrote: > > On May 8, 2008, at 12:44 PM, Tony Chiang wrote: > > > Well, that is not exactly true... > > > > On Thu, May 8, 2008 at 8:26 PM, Kasper Daniel Hansen < > khansen@stat.berkeley.edu > > > wrote: > > This problem is really only for people using Graphviz on Windows > > using a binary version. > > > > If you compile Rgraphviz (say on Linux or Mac OS X) you just install > > whatever version of graphviz you need and then compile against it. > > > > You are correct if someone is going to build Rgraphviz from source, > > but there are people who do use Max OS X as well as some Linux users > > who do just download the binary files. > > > > In general, I have work exclusively on a Mac with Tiger, and I > > usually download the binary stable version of R from Simon's > > homepage while I always build the development version of R from > > source. This time around, I had to compile Rgraphviz locally for > > both R and R-devel to get anything to work. This is after upgrading > > all the compilers, gcc, graphviz, etc. > > > > I don't know if this is what is meant for the general user's of R. > > Most people who use R where I work would not be able to do all this > > (some could and would). > > In case my position was unclear: I totally agree with you on this one: > Rgraphviz has been made much more difficult to install on Windows. > Possibly also on OS X, although I haven't checked (your comment seems > to indicate it though). On Linux I would have to disagree: no-one (as > far as I know) provides binaries for Linux. And these changes have > happened without much fanfare. > > Kasper > > > > > > > > > The problem is really for Windows users using the BINARY version of > > the RGraphviz package (which most people do I think). You then need > > the exact same binary version of Graphviz as was used to create the > > RGraphviz binary version. This is apparently 2.16. > > > > Let me iterate: the graphviz >= 12 is only really for people > > compiling from source. > > > > Now, this is a major change from earlier where Graphviz 2.2 was > > included with the RGraphviz package for Windows users. This was > > great - no-one had to do anything to get it going. Unfortunately > > that package is beginning to get outdated and it is (for various > > reasons) very difficult to do that trick again. > > > > So someone decided to make people install the binary version of > > Graphviz 2.16 for Windows users. I agree with Jenny that this is a > > major change and it should be kind of highlighted. The fact that she > > has missed this information is probably an indication that something > > need to be added somewhere. My guess is that this was overlooked? > > Especially since it is a very specific version of graphviz requested > > and not just any >= 2.12. > > > > Kasper > > > > > > On May 8, 2008, at 11:50 AM, Jenny Drnevich wrote: > > > > Hi Martin, > > > > I just ran into this problem myself, and I'm a little confused as to > > your response. I was looking at all the documentation/vignettes for > > Rgraphviz, and it's not very clear or explicit either. First of all, > > there is very little mention of needing graphviz in Rgraphviz; In > > Details it does say SystemRequirements - Graphviz version >= 2.2 , > > but that's all. It would be useful if in one or both of the vignettes > > at the beginning there was a description that an external program was > > needed, and where to go to download it. The only mention of it all in > > either vignette is at the end in the SessionInfo section, which has > > hard-coded "together with version 2.12 of graphviz." > > > > My other confusion is what version of graphviz is needed. The > > SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes > > is obviously wrong and a hold-over from the previous version. You say > > below Rgraphviz is built with graphviz 2.16. However, the graphviz > > website (http://www.graphviz.org/Download_windows.php) shows two > > stable versions, 2.16.1.static and 2.18. The SystemRequirements is > > obviously wrong since the developmental version is only 2.19. And I > > wasn't sure what you were referring to below when you said > > > > The version of graphviz installed on your computer has to match the > > version used to build Rgraphviz, so 2.18 will not work. > > > > I assume the 2.18 is referring to the graphviz 2.18 and not a typo of > > Rgraphviz 1.18? There wasn't any mention of a higher version of > > graphviz in your e-mail, but now it makes since after visiting the > > graphviz website and noticing the ARCHIVE in the link you posted. So > > I guess that after all, I need to have graphviz 2.16 installed (AND > > in my path - another point for the vignette) ? I just wanted to > > point out that this information is apparently not associated with > > Rgraphviz at all, except for this post, and will likely cause other > > users problems. > > > > Oh, and I just noticed this Note to Windows users on the graphviz > > page: > > > > Meanwhile, if you get error messages like: > > "The application has failed to start because somefilename.dll was not > > found. Re-installing the application may fix this problem." > > please click this > > < > http://www.microsoft.com/downloads/details.aspx?familyid=32bc1bee- a3f9-4c13-9c99-220b62a191ee&displaylang=en > > >link > > and install Microsoft Visual C++ 2005 Redistributable Package (x86). > > > > I had that problem as well. Good to see how to fix it. Overall, a > > VERY difficult packages for (windows) users to get running. > > > > > > Thanks, > > Jenny > > > > At 08:02 AM 5/8/2008, Martin Morgan wrote: > > Hi -- > > > > 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 > > > > > > LiGang <luzifer.li@gmail.com> writes: > > > > I have problems loading the Rgraphviz package under Windows > > with the newest > > version of R. > > > > I installed Rgraphviz package using biocLite("Rgraphviz") method and > > the > > package version of Rgraphviz is 1.18.0.(Also, I have installed the > > "Rgraphviz" version 1.16.0 with no trouble at all) > > > > > > > > Here is the error message I am getting: > > > > ---- > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > > unable to load shared library > > 'C:/PROGRA~1/R/R-27~1.0RC/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' > > ----- > > > > The version of Bioconductor is 2.2. > > > > And here is the session info: > > ############ > > R version 2.7.0 (2008-04-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=Chinese_People's Republic of China. > > 936;LC_CTYPE=Chinese_People's > > Republic of China.936;LC_MONETARY=Chinese_People's Republic of > > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets > > methods > > base > > > > other attached packages: > > [1] graph_1.18.0 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.10 tools_2.7.0 > > ############ > > > > Thanks! > > > > --- > > LiGang > > > > [[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 > > > > -- > > 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 > > > > _______________________________________________ > > 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@uiuc.edu > > [[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 > > > > _______________________________________________ > > 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 > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Jenny Drnevich wrote: > Hi Martin, > > I just ran into this problem myself, and I'm a little confused as to > your response. I was looking at all the documentation/vignettes for > Rgraphviz, and it's not very clear or explicit either. First of all, > there is very little mention of needing graphviz in Rgraphviz; In > Details it does say SystemRequirements - Graphviz version >= 2.2 , > but that's all. It would be useful if in one or both of the vignettes > at the beginning there was a description that an external program was > needed, and where to go to download it. The only mention of it all in > either vignette is at the end in the SessionInfo section, which has > hard-coded "together with version 2.12 of graphviz." > Hi Jenny, I am not sure that installation instructions for a package should be in the vignette. First, you will not be able to read it unless you are able to install the package (of course you can always download the pdf from somewhere), and second, the main point of a vignette in a Bioconductor package is to give a short introduction to the functionality provided and, if possible, a simple use case. With the source code of the package comes a README file that tells you about all the system requirements and contains a detailed instruction how to install the package on Windows, and that seems to be the standard way of documenting these things in the software world. > My other confusion is what version of graphviz is needed. The > SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes > is obviously wrong and a hold-over from the previous version. That should indeed be fixed. I will take a look at this. > You say > below Rgraphviz is built with graphviz 2.16. However, the graphviz > website (http://www.graphviz.org/Download_windows.php) shows two > stable versions, 2.16.1.static and 2.18. The SystemRequirements is > obviously wrong since the developmental version is only 2.19. And I > wasn't sure what you were referring to below when you said > > >> The version of graphviz installed on your computer has to match the >> version used to build Rgraphviz, so 2.18 will not work. >> > > I assume the 2.18 is referring to the graphviz 2.18 and not a typo of > Rgraphviz 1.18? There wasn't any mention of a higher version of > graphviz in your e-mail, but now it makes since after visiting the > graphviz website and noticing the ARCHIVE in the link you posted. So > I guess that after all, I need to have graphviz 2.16 installed (AND > in my path - another point for the vignette) ? I just wanted to > point out that this information is apparently not associated with > Rgraphviz at all, except for this post, and will likely cause other > users problems. > > Oh, and I just noticed this Note to Windows users on the graphviz page: > > Meanwhile, if you get error messages like: > "The application has failed to start because somefilename.dll was not > found. Re-installing the application may fix this problem." > please click this > <http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en">link > and install Microsoft Visual C++ 2005 Redistributable Package (x86). > This is also in the README file... It would be helpful if one could point to this file directly on the Bioc packages webpage. There already is the yellow box containing the default To install this package, start R and enter: source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") message, and I wonder if there is a way to customize its content. Cheers, Florian > I had that problem as well. Good to see how to fix it. Overall, a > VERY difficult packages for (windows) users to get running. > > > Thanks, > Jenny > > At 08:02 AM 5/8/2008, Martin Morgan wrote: > >> Hi -- >> >> 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 >> >> >> LiGang <luzifer.li at="" gmail.com=""> writes: >> >> >>> I have problems loading the Rgraphviz package under Windows >>> >> with the newest >> >>> version of R. >>> >>> I installed Rgraphviz package using biocLite("Rgraphviz") method and the >>> package version of Rgraphviz is 1.18.0.(Also, I have installed the >>> "Rgraphviz" version 1.16.0 with no trouble at all) >>> >>> >>> >>> Here is the error message I am getting: >>> >>> ---- >>> Error in inDL(x, as.logical(local), as.logical(now), ...) : >>> unable to load shared library >>> 'C:/PROGRA~1/R/R-27~1.0RC/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' >>> ----- >>> >>> The version of Bioconductor is 2.2. >>> >>> And here is the session info: >>> ############ >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=Chinese_People's Republic of China.936;LC_CTYPE=Chinese_People's >>> Republic of China.936;LC_MONETARY=Chinese_People's Republic of >>> China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] graph_1.18.0 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.10 tools_2.7.0 >>> ############ >>> >>> Thanks! >>> >>> --- >>> LiGang >>> >>> [[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 >> >> -- >> 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 >> >> _______________________________________________ >> 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 uiuc.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 > -- Florian Hahne, PhD Computational Biology Program Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-3148 fhahne at fhcrc.org
ADD REPLY •
0
Entering edit mode
Hi Jenny (and Kasper, and ...) -- Jenny Drnevich wrote: > Hi Martin, > > I just ran into this problem myself, and I'm a little confused as to > your response. I was looking at all the documentation/vignettes for > Rgraphviz, and it's not very clear or explicit either. First of all, > there is very little mention of needing graphviz in Rgraphviz; In > > Details it does say SystemRequirements - Graphviz version >= 2.2 , but > that's all. It would be useful if in one or both of the vignettes at the > beginning there was a description that an external program was needed, > and where to go to download it. The only mention of it all in either > vignette is at the end in the SessionInfo section, which has hard- coded > "together with version 2.12 of graphviz." > > My other confusion is what version of graphviz is needed. The > SystemRequirements says >= 2.2. The hard-coded 2.12 in the vignettes is > obviously wrong and a hold-over from the previous version. You say below > Rgraphviz is built with graphviz 2.16. However, the graphviz website ( > http://www.graphviz.org/Download_windows.php) shows two stable versions, > 2.16.1.static and 2.18. The SystemRequirements is obviously wrong since > the developmental version is only 2.19. And I wasn't sure what you were > referring to below when you said Version numbers are confusing but 2.2 < 2.16 (i.e. version 2.16 is more recent than 2.2) because 2 < 16. >> The version of graphviz installed on your computer has to match the >> version used to build Rgraphviz, so 2.18 will not work. > > I assume the 2.18 is referring to the graphviz 2.18 and not a typo of > Rgraphviz 1.18? There wasn't any mention of a higher version of graphviz yep, only graphviz 2.16 will work with Rgraphviz 1.18 installed with biocLite. > in your e-mail, but now it makes since after visiting the graphviz > website and noticing the ARCHIVE in the link you posted. So I guess that > after all, I need to have graphviz 2.16 installed (AND in my path - > another point for the vignette) ? I just wanted to point out that this > information is apparently not associated with Rgraphviz at all, except > for this post, and will likely cause other users problems. > > Oh, and I just noticed this Note to Windows users on the graphviz page: > > Meanwhile, if you get error messages like: > "The application has failed to start because somefilename.dll was not > found. Re-installing the application may fix this problem." > please click this link > <http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en"> > and install Microsoft Visual C++ 2005 Redistributable Package (x86). > > I had that problem as well. Good to see how to fix it. Overall, a VERY > difficult packages for (windows) users to get running. > Yep, I agree. It's also a bit of a nightmare from the package maintainer perspective, because there are all these places (which you point out) where the information needs to be kept current, and the correct information depends on the machine used to build the package (i.e., not under the maintainer's control). We'll try to work with the maintainer to arrive at some more robust solution. Martin > Thanks, > Jenny > > At 08:02 AM 5/8/2008, Martin Morgan wrote: >> Hi -- >> >> 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 >> >> >> LiGang <luzifer.li at="" gmail.com=""> writes: >> >> > I have problems loading the Rgraphviz package under Windows with >> the newest >> > version of R. >> > >> > I installed Rgraphviz package using biocLite("Rgraphviz") method and the >> > package version of Rgraphviz is 1.18.0.(Also, I have installed the >> > "Rgraphviz" version 1.16.0 with no trouble at all) >> > >> > >> > >> > Here is the error message I am getting: >> > >> > ---- >> > Error in inDL(x, as.logical(local), as.logical(now), ...) : >> > unable to load shared library >> > 'C:/PROGRA~1/R/R-27~1.0RC/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' >> > ----- >> > >> > The version of Bioconductor is 2.2. >> > >> > And here is the session info: >> > ############ >> > R version 2.7.0 (2008-04-22) >> > i386-pc-mingw32 >> > >> > locale: >> > LC_COLLATE=Chinese_People's Republic of >> China.936;LC_CTYPE=Chinese_People's >> > Republic of China.936;LC_MONETARY=Chinese_People's Republic of >> > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 >> > >> > attached base packages: >> > [1] grid stats graphics grDevices utils datasets methods >> > base >> > >> > other attached packages: >> > [1] graph_1.18.0 >> > >> > loaded via a namespace (and not attached): >> > [1] cluster_1.11.10 tools_2.7.0 >> > ############ >> > >> > Thanks! >> > >> > --- >> > LiGang >> > >> > [[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 >> >> -- >> 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 >> >> _______________________________________________ >> 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 uiuc.edu > -- 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
ADD REPLY •
0
Entering edit mode
Thanks Martin (and Kasper, and ...), >Version numbers are confusing but 2.2 < 2.16 (i.e. version 2.16 is >more recent than 2.2) because 2 < 16. This was just recently pointed out on the list, but my brain did not incorporate it! My biological/statistical training see it mathematically: 2.2 > 2.16. Maybe now after this second reminder I'll remember it... :) Jenny >>>The version of graphviz installed on your computer has to match the >>>version used to build Rgraphviz, so 2.18 will not work. >>I assume the 2.18 is referring to the graphviz 2.18 and not a typo >>of Rgraphviz 1.18? There wasn't any mention of a higher version of graphviz > >yep, only graphviz 2.16 will work with Rgraphviz 1.18 installed with biocLite. > >>in your e-mail, but now it makes since after visiting the graphviz >>website and noticing the ARCHIVE in the link you posted. So I guess >>that after all, I need to have graphviz 2.16 installed (AND in my >>path - another point for the vignette) ? I just wanted to point >>out that this information is apparently not associated with >>Rgraphviz at all, except for this post, and will likely cause other >>users problems. >>Oh, and I just noticed this Note to Windows users on the graphviz page: >>Meanwhile, if you get error messages like: >>"The application has failed to start because somefilename.dll was >>not found. Re-installing the application may fix this problem." >>please click this link >><http: www.microsoft.com="" downloads="" details.aspx?familyid="32bc1bee-" a3f9-4c13-9c99-220b62a191ee&displaylang="en"> >>and install Microsoft Visual C++ 2005 Redistributable Package (x86). >>I had that problem as well. Good to see how to fix it. Overall, a >>VERY difficult packages for (windows) users to get running. > >Yep, I agree. It's also a bit of a nightmare from the package >maintainer perspective, because there are all these places (which >you point out) where the information needs to be kept current, and >the correct information depends on the machine used to build the >package (i.e., not under the maintainer's control). > >We'll try to work with the maintainer to arrive at some more robust solution. > >Martin > >>Thanks, >>Jenny >>At 08:02 AM 5/8/2008, Martin Morgan wrote: >>>Hi -- >>> >>>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 >>> >>> >>>LiGang <luzifer.li at="" gmail.com=""> writes: >>> >>> > I have problems loading the Rgraphviz package under Windows with >>>the newest >>> > version of R. >>> > >>> > I installed Rgraphviz package using biocLite("Rgraphviz") method and the >>> > package version of Rgraphviz is 1.18.0.(Also, I have installed the >>> > "Rgraphviz" version 1.16.0 with no trouble at all) >>> > >>> > >>> > >>> > Here is the error message I am getting: >>> > >>> > ---- >>> > Error in inDL(x, as.logical(local), as.logical(now), ...) : >>> > unable to load shared library >>> > 'C:/PROGRA~1/R/R-27~1.0RC/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' >>> > ----- >>> > >>> > The version of Bioconductor is 2.2. >>> > >>> > And here is the session info: >>> > ############ >>> > R version 2.7.0 (2008-04-22) >>> > i386-pc-mingw32 >>> > >>> > locale: >>> > LC_COLLATE=Chinese_People's Republic of >>> China.936;LC_CTYPE=Chinese_People's >>> > Republic of China.936;LC_MONETARY=Chinese_People's Republic of >>> > China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936 >>> > >>> > attached base packages: >>> > [1] grid stats graphics grDevices utils datasets methods >>> > base >>> > >>> > other attached packages: >>> > [1] graph_1.18.0 >>> > >>> > loaded via a namespace (and not attached): >>> > [1] cluster_1.11.10 tools_2.7.0 >>> > ############ >>> > >>> > Thanks! >>> > >>> > --- >>> > LiGang >>> > >>> > [[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 >>> >>>-- >>>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 >>> >>>_______________________________________________ >>>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 uiuc.edu > > >-- >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 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 uiuc.edu
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 573 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6