error installing Rgraphviz
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Mark Miller ▴ 10
@mark-miller-5307
Last seen 7.1 years ago
I am attempting to install the package 'Rgraphviz' in R version 2.15.0 on a PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). However, when I type 'library('Rgraphviz')' I keep getting a pop-up error message stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start because libcdt-4.dll is missing from your computer. Try reinstalling the program to fix the problem.' Within R I get an error message stating that there is no package 'Rgraphviz'. I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' which I believe I downloaded from the link in an R post found here: http://r.789695.n4.nabble.com/Rgraphviz-install-td878526.html The actual link within the above R post was: http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1. msi The directory to Graphviz on my computer is 'c:\Program Files (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the folder 'c:\Program Files (x86)\Graphviz2.20\bin'. The following appears at the end of my path statement 'Program Files (x86)\Graphvis2.20\bin' and is also displayed when I type 'C:\echo %PATH%' in a command window. The directory to R on my computer is 'c:\Program Files\R\R-2.15.0\'. When I try to install 'Rgraphviz' I get the following messages within R: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.4, ?biocLite for help > biocLite("Rgraphviz") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'Rgraphviz' trying URL ' http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.1 5/Rgraphviz_1.34.0.zip ' Content type 'application/zip' length 936601 bytes (914 Kb) opened URL downloaded 914 Kb package ‘Rgraphviz’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Mark W Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages Warning message: installed directory not writable, cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', 'survival' > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the package 'Rgraphviz' does not appear in the R library in 'c:\Program Files\R\R-2.15.0\library'. Rather 'Rgraphviz' appears in 'C:\users\Mark W Miller\Documents\R\win-library\2.15' I have copied and pasted the 'Rgraphviz' folder from 'C:\users\Mark W Miller\Documents\R\win-library\2.15' into 'C:\Program Files\R\R-2.15.0\library\'. Then inside R I type 'library('Rgraphviz')' and get the following message in a pop-up window: 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start because libcdt-4.dll is missing from your computer. Try reinstalling the program to fix the problem.' and the following messages within R: > library('Rgraphviz') Loading required package: graph Loading required package: grid Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: call: value[[3L]](cond) error: unable to load shared object 'C:/Users/Mark W Miller/Documents/R/win-library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. Check that (1) graphviz is installed on your system; (2) the installed version of graphviz matches '2.20.3'; this is the version used to build this Rgraphviz package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin' directory is in the system 'PATH' variable. See additional instructions in the 'README' file of the Rgraphviz 'source' distribution, available at http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask further questions on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html Error: package/namespace load failed for ‘Rgraphviz’ > The file 'C:\Users\Mark W Miller\Documents\R\win-library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' does exist in that folder and in the folder where I copied and pasted it into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. In addition to the steps described above I have tried countless variations over approximately 8 hours, including uninstalling R and re-installing it. During one reboot maybe 4 hours into this process I even got an error message on start-up and almost everything on my desktop had disappeared. I restarted the computer again and my normal desktop was restored. (I found a post on the internet describing something similar when trying to install 'Rgraphviz' but I do not know whether my experience was related to that previous incident.) I am hoping someone can provide detailed step-by-step instructions on how to install the package Rgraphviz and/or identify where I am making a mistake based on the information I have provided. I have tried to include here as much information as I can think of. If I can include additional helpful information please let me know. I wonder whether the above warning message is related to why I cannot install 'Rgraphviz': 'Warning message: installed directory not writable, cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', 'survival''. I have not previously posted on this forum. Hopefully I am following protocol. Thank you for any advice. Mark W. Miller [[alternative HTML version deleted]]
Rgraphviz PROcess BiocInstaller Rgraphviz PROcess BiocInstaller • 1.5k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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Hi Mark, On Sun, May 27, 2012 at 4:13 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > I am attempting to install the package 'Rgraphviz' in R version 2.15.0 on a > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). ?However, > when I type 'library('Rgraphviz')' I keep getting a pop-up error message > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start > because libcdt-4.dll is missing from your computer. Try reinstalling the > program to fix the problem.' Within R I get an error message stating that > there is no package 'Rgraphviz'. > > I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' which I > believe I downloaded from the link in an R post found here: > > http://r.789695.n4.nabble.com/Rgraphviz-install-td878526.html > > The actual link within the above R post was: > > http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3. 1.msi > > > > The directory to Graphviz on my computer is 'c:\Program Files > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the folder > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following appears at the > end of my path statement 'Program Files (x86)\Graphvis2.20\bin' and is also > displayed when I type 'C:\echo %PATH%' in a command window. > Can you send the full output of the echo %PATH% command? Note that "Graphviz" is mis-spelled above. Could that be the problem? Also note that if you set your PATH in Control Panel, you need to start a new command window after making the change, because the change will not be reflected in any currently open command windows. > The directory to R on my computer is 'c:\Program Files\R\R-2.15.0\'. > > When I try to install 'Rgraphviz' I get the following messages within R: > > >> source("http://bioconductor.org/biocLite.R") > > BiocInstaller version 1.4.4, ?biocLite for help > >> biocLite("Rgraphviz") > > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Installing package(s) 'Rgraphviz' > trying URL ' > http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2 .15/Rgraphviz_1.34.0.zip > ' > Content type 'application/zip' length 936601 bytes (914 Kb) > opened URL > downloaded 914 Kb > > package ?Rgraphviz? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > ? ? ? ?C:\Users\Mark W > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages > Warning message: > installed directory not writable, cannot update packages 'foreign', 'MASS', > ?'mgcv', 'nlme', 'survival' > >> > > > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the package > 'Rgraphviz' does not appear in the R library in 'c:\Program > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in 'C:\users\Mark W > Miller\Documents\R\win-library\2.15' > This is ok. > I have copied and pasted the 'Rgraphviz' folder from 'C:\users\Mark W > Miller\Documents\R\win-library\2.15' into 'C:\Program > Files\R\R-2.15.0\library\'. You do not need to do this. > > Then inside R I type 'library('Rgraphviz')' and get the following message > in a pop-up window: > > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start because > libcdt-4.dll is missing from your computer. Try reinstalling the program to > fix the problem.' > > and the following messages within R: > > >> library('Rgraphviz') > > Loading required package: graph > Loading required package: grid > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > ?call: value[[3L]](cond) > ?error: unable to load shared object 'C:/Users/Mark W > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': > ?LoadLibrary failure: ?The specified module could not be found. > > > ?Check that (1) graphviz is installed on your system; (2) the > ?installed version of graphviz matches '2.20.3'; this is the version > ?used to build this Rgraphviz package; (3) graphviz is accessible to > ?R, e.g., the path to the graphviz 'bin' directory is in the system > ?'PATH' variable. ?See additional instructions in the 'README' file of > ?the Rgraphviz 'source' distribution, available at > > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html > > ?Ask further questions on the Bioconductor mailing list > > ?http://bioconductor.org/docs/mailList.html > > > Error: package/namespace load failed for ?Rgraphviz? > >> > > > The file 'C:\Users\Mark W > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' does > exist in that folder and in the folder where I copied and pasted it > into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. > > > In addition to the steps described above I have tried countless variations > over approximately 8 hours, including uninstalling R and re- installing it. > > During one reboot maybe 4 hours into this process I even got an error > message on start-up and almost everything on my desktop had disappeared. ?I > restarted the computer again and my normal desktop was restored. ?(I found > a post on the internet describing something similar when trying to install > 'Rgraphviz' but I do not know whether my experience was related to that > previous incident.) > > I am hoping someone can provide detailed step-by-step instructions on how > to install the package Rgraphviz and/or identify where I am making a > mistake based on the information I have provided. ?I have tried to include > here as much information as I can think of. ?If I can include additional > helpful information please let me know. > > I wonder whether the above warning message is related to why I cannot > install 'Rgraphviz': 'Warning message: installed directory not writable, > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', 'survival''. > No. That is just biocLite() telling you that those packages couldn't be updated because they live in a directory that you can't write to. If you log in as an admin user you can update those packages and make that message go away, or you can just ignore it. Dan > I have not previously posted on this forum. ?Hopefully I am following > protocol. > > Thank you for any advice. > > Mark W. Miller > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dan Tenenbaum ★ 8.2k
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[cc'ing bioconductor list so others can benefit from this] On Mon, May 28, 2012 at 1:16 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > > Hi Dan, > > Thank you for the reply. > > Below is my current PATH statement: > > C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files > (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program Files\Dell\DW > WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files > (x86)\AMD > APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32 \Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program > Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program > Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth > Software\syswow64;C:\Program Files (x86)\Windows > Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20 > The directory that should be in your PATH is: C:\Program Files (x86)\Graphviz2.20\bin (note the \bin at the end). That is where the DLL is located that Rgraphviz is complaining about, as well as other files it needs. > You are correct that I had misspelled 'Graphviz' earlier. ?I think I have > spelled it correctly now. ?I tried to check whether that was the problem by > first correcting the spelling in the PATH statement and then trying to > re-install Rgraphviz. ?However, I still received errors. > > Next I uninstalled Graphviz. ?I noted that I had to manually remove Graphviz > from the PATH statement. ?Then I re-installed Graphviz and added it back to > the PATH statement. ?I still receive the pop-up error message described > earlier after re-installing Rgraphviz. > > In between uninstalling and re-installing or between correcting, removing > and adding text to the PATH statement I performed frequent reboots followed > by use of the 'echo %PATH%' command statement to check the PATH. > You do not need to reboot your machine after chaning the PATH. You just need to close and reopen the command prompt window. > I think this covers your earlier suggestions. ?Sorry if I overlooked any. > > I was hoping to install Rgraphviz because I was hoping to explore R's > ability to act as a GIS system and a reference book on the subject used > Rgraphviz in at least one example file. ?I do not know how frequently > Rgraphviz is used by that reference, so I do not yet know how critical > Rgraphviz will be for me in pursuing that exploration. > > Regardless, thank you for your help. ?Let me know if I can provide > additional useful information. > If the above suggestions do not help, please send the output of the sessionInfo() command. I'm wondering if you are running 32- or 64-bit R. If 64, then you'll need to install a different version of Graphviz. Dan > Mark > > > > > > > On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> Hi Mark, >> >> On Sun, May 27, 2012 at 4:13 PM, Mark Miller >> <mark.wayne.miller at="" gmail.com=""> wrote: >> > I am attempting to install the package 'Rgraphviz' in R version 2.15.0 >> > on a >> > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). >> > ?However, >> > when I type 'library('Rgraphviz')' I keep getting a pop-up error message >> > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't >> > start >> > because libcdt-4.dll is missing from your computer. Try reinstalling the >> > program to fix the problem.' Within R I get an error message stating >> > that >> > there is no package 'Rgraphviz'. >> > >> > I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' which I >> > believe I downloaded from the link in an R post found here: >> > >> > http://r.789695.n4.nabble.com/Rgraphviz-install-td878526.html >> > >> > The actual link within the above R post was: >> > >> > >> > http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20 .3.1.msi >> > >> > >> > >> > The directory to Graphviz on my computer is 'c:\Program Files >> > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the folder >> > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following appears at the >> > end of my path statement 'Program Files (x86)\Graphvis2.20\bin' and is >> > also >> > displayed when I type 'C:\echo %PATH%' in a command window. >> > >> >> Can you send the full output of the echo %PATH% command? >> Note that "Graphviz" is mis-spelled above. Could that be the problem? >> >> >> Also note that if you set your PATH in Control Panel, you need to >> start a new command window after making the change, because the change >> will not be reflected in any currently open command windows. >> >> > The directory to R on my computer is 'c:\Program Files\R\R-2.15.0\'. >> > >> > When I try to install 'Rgraphviz' I get the following messages within R: >> > >> > >> >> source("http://bioconductor.org/biocLite.R") >> > >> > BiocInstaller version 1.4.4, ?biocLite for help >> > >> >> biocLite("Rgraphviz") >> > >> > BioC_mirror: http://bioconductor.org >> > Using R version 2.15, BiocInstaller version 1.4.4. >> > Installing package(s) 'Rgraphviz' >> > trying URL ' >> > >> > http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contri b/2.15/Rgraphviz_1.34.0.zip >> > ' >> > Content type 'application/zip' length 936601 bytes (914 Kb) >> > opened URL >> > downloaded 914 Kb >> > >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >> > >> > The downloaded binary packages are in >> > ? ? ? ?C:\Users\Mark W >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages >> > Warning message: >> > installed directory not writable, cannot update packages 'foreign', >> > 'MASS', >> > ?'mgcv', 'nlme', 'survival' >> > >> >> >> > >> > >> > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the >> > package >> > 'Rgraphviz' does not appear in the R library in 'c:\Program >> > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in 'C:\users\Mark >> > W >> > Miller\Documents\R\win-library\2.15' >> > >> >> This is ok. >> >> >> > I have copied and pasted the 'Rgraphviz' folder from 'C:\users\Mark W >> > Miller\Documents\R\win-library\2.15' into 'C:\Program >> > Files\R\R-2.15.0\library\'. >> >> >> You do not need to do this. >> >> > >> > Then inside R I type 'library('Rgraphviz')' and get the following >> > message >> > in a pop-up window: >> > >> > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start >> > because >> > libcdt-4.dll is missing from your computer. Try reinstalling the program >> > to >> > fix the problem.' >> > >> > and the following messages within R: >> > >> > >> >> library('Rgraphviz') >> > >> > Loading required package: graph >> > Loading required package: grid >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >> > ?call: value[[3L]](cond) >> > ?error: unable to load shared object 'C:/Users/Mark W >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >> > ?LoadLibrary failure: ?The specified module could not be found. >> > >> > >> > ?Check that (1) graphviz is installed on your system; (2) the >> > ?installed version of graphviz matches '2.20.3'; this is the version >> > ?used to build this Rgraphviz package; (3) graphviz is accessible to >> > ?R, e.g., the path to the graphviz 'bin' directory is in the system >> > ?'PATH' variable. ?See additional instructions in the 'README' file of >> > ?the Rgraphviz 'source' distribution, available at >> > >> > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> > >> > ?Ask further questions on the Bioconductor mailing list >> > >> > ?http://bioconductor.org/docs/mailList.html >> > >> > >> > Error: package/namespace load failed for ?Rgraphviz? >> > >> >> >> > >> > >> > The file 'C:\Users\Mark W >> > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' >> > does >> > exist in that folder and in the folder where I copied and pasted it >> > into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. >> > >> > >> > In addition to the steps described above I have tried countless >> > variations >> > over approximately 8 hours, including uninstalling R and re- installing >> > it. >> > >> > During one reboot maybe 4 hours into this process I even got an error >> > message on start-up and almost everything on my desktop had disappeared. >> > ?I >> > restarted the computer again and my normal desktop was restored. ?(I >> > found >> > a post on the internet describing something similar when trying to >> > install >> > 'Rgraphviz' but I do not know whether my experience was related to that >> > previous incident.) >> > >> > I am hoping someone can provide detailed step-by-step instructions on >> > how >> > to install the package Rgraphviz and/or identify where I am making a >> > mistake based on the information I have provided. ?I have tried to >> > include >> > here as much information as I can think of. ?If I can include additional >> > helpful information please let me know. >> > >> > I wonder whether the above warning message is related to why I cannot >> > install 'Rgraphviz': 'Warning message: installed directory not writable, >> > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', 'survival''. >> > >> >> No. That is just biocLite() telling you that those packages couldn't >> be updated because they live in a directory that you can't write to. >> If you log in as an admin user you can update those packages and make >> that message go away, or you can just ignore it. >> >> Dan >> >> >> > I have not previously posted on this forum. ?Hopefully I am following >> > protocol. >> > >> > Thank you for any advice. >> > >> > Mark W. Miller >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Dan Tenenbaum ★ 8.2k
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On Mon, May 28, 2012 at 1:36 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > > Thanks, Dan. > > Unfortunately, that does not solve the problem. > Are you getting the same error message? What is the output of R's sessionInfo() command? What happens if you type: neato -V at a Windows command prompt? Dan > Mark > > > > > On Mon, May 28, 2012 at 12:24 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> [cc'ing bioconductor list so others can benefit from this] >> >> On Mon, May 28, 2012 at 1:16 PM, Mark Miller >> <mark.wayne.miller at="" gmail.com=""> wrote: >> > >> > Hi Dan, >> > >> > Thank you for the reply. >> > >> > Below is my current PATH statement: >> > >> > C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program >> > Files >> > (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program >> > Files\Dell\DW >> > WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files >> > (x86)\AMD >> > >> > APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\Syste m32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program >> > Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program >> > Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth >> > Software\syswow64;C:\Program Files (x86)\Windows >> > Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20 >> > >> >> The directory that should be in your PATH is: >> >> C:\Program Files (x86)\Graphviz2.20\bin >> >> (note the \bin at the end). That is where the DLL is located that >> Rgraphviz is complaining about, as well as other files it needs. >> >> >> >> > You are correct that I had misspelled 'Graphviz' earlier. ?I think I >> > have >> > spelled it correctly now. ?I tried to check whether that was the problem >> > by >> > first correcting the spelling in the PATH statement and then trying to >> > re-install Rgraphviz. ?However, I still received errors. >> > >> > Next I uninstalled Graphviz. ?I noted that I had to manually remove >> > Graphviz >> > from the PATH statement. ?Then I re-installed Graphviz and added it back >> > to >> > the PATH statement. ?I still receive the pop-up error message described >> > earlier after re-installing Rgraphviz. >> > >> > In between uninstalling and re-installing or between correcting, >> > removing >> > and adding text to the PATH statement I performed frequent reboots >> > followed >> > by use of the 'echo %PATH%' command statement to check the PATH. >> > >> >> You do not need to reboot your machine after chaning the PATH. You >> just need to close and reopen the command prompt window. >> >> > I think this covers your earlier suggestions. ?Sorry if I overlooked >> > any. >> > >> > I was hoping to install Rgraphviz because I was hoping to explore R's >> > ability to act as a GIS system and a reference book on the subject used >> > Rgraphviz in at least one example file. ?I do not know how frequently >> > Rgraphviz is used by that reference, so I do not yet know how critical >> > Rgraphviz will be for me in pursuing that exploration. >> > >> > Regardless, thank you for your help. ?Let me know if I can provide >> > additional useful information. >> > >> >> If the above suggestions do not help, please send the output of the >> sessionInfo() command. I'm wondering if you are running 32- or 64-bit >> R. If 64, then you'll need to install a different version of Graphviz. >> >> Dan >> >> >> > Mark >> > >> > >> > >> > >> > >> > >> > On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> Hi Mark, >> >> >> >> On Sun, May 27, 2012 at 4:13 PM, Mark Miller >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> > I am attempting to install the package 'Rgraphviz' in R version >> >> > 2.15.0 >> >> > on a >> >> > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). >> >> > ?However, >> >> > when I type 'library('Rgraphviz')' I keep getting a pop-up error >> >> > message >> >> > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't >> >> > start >> >> > because libcdt-4.dll is missing from your computer. Try reinstalling >> >> > the >> >> > program to fix the problem.' Within R I get an error message stating >> >> > that >> >> > there is no package 'Rgraphviz'. >> >> > >> >> > I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' >> >> > which I >> >> > believe I downloaded from the link in an R post found here: >> >> > >> >> > http://r.789695.n4.nabble.com/Rgraphviz-install-td878526.html >> >> > >> >> > The actual link within the above R post was: >> >> > >> >> > >> >> > >> >> > http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2 .20.3.1.msi >> >> > >> >> > >> >> > >> >> > The directory to Graphviz on my computer is 'c:\Program Files >> >> > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the >> >> > folder >> >> > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following appears at >> >> > the >> >> > end of my path statement 'Program Files (x86)\Graphvis2.20\bin' and >> >> > is >> >> > also >> >> > displayed when I type 'C:\echo %PATH%' in a command window. >> >> > >> >> >> >> Can you send the full output of the echo %PATH% command? >> >> Note that "Graphviz" is mis-spelled above. Could that be the problem? >> >> >> >> >> >> Also note that if you set your PATH in Control Panel, you need to >> >> start a new command window after making the change, because the change >> >> will not be reflected in any currently open command windows. >> >> >> >> > The directory to R on my computer is 'c:\Program Files\R\R-2.15.0\'. >> >> > >> >> > When I try to install 'Rgraphviz' I get the following messages within >> >> > R: >> >> > >> >> > >> >> >> source("http://bioconductor.org/biocLite.R") >> >> > >> >> > BiocInstaller version 1.4.4, ?biocLite for help >> >> > >> >> >> biocLite("Rgraphviz") >> >> > >> >> > BioC_mirror: http://bioconductor.org >> >> > Using R version 2.15, BiocInstaller version 1.4.4. >> >> > Installing package(s) 'Rgraphviz' >> >> > trying URL ' >> >> > >> >> > >> >> > http://www.bioconductor.org/packages/2.10/bioc/bin/windows/con trib/2.15/Rgraphviz_1.34.0.zip >> >> > ' >> >> > Content type 'application/zip' length 936601 bytes (914 Kb) >> >> > opened URL >> >> > downloaded 914 Kb >> >> > >> >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >> >> > >> >> > The downloaded binary packages are in >> >> > ? ? ? ?C:\Users\Mark W >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages >> >> > Warning message: >> >> > installed directory not writable, cannot update packages 'foreign', >> >> > 'MASS', >> >> > ?'mgcv', 'nlme', 'survival' >> >> > >> >> >> >> >> > >> >> > >> >> > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the >> >> > package >> >> > 'Rgraphviz' does not appear in the R library in 'c:\Program >> >> > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in >> >> > 'C:\users\Mark >> >> > W >> >> > Miller\Documents\R\win-library\2.15' >> >> > >> >> >> >> This is ok. >> >> >> >> >> >> > I have copied and pasted the 'Rgraphviz' folder from 'C:\users\Mark W >> >> > Miller\Documents\R\win-library\2.15' into 'C:\Program >> >> > Files\R\R-2.15.0\library\'. >> >> >> >> >> >> You do not need to do this. >> >> >> >> > >> >> > Then inside R I type 'library('Rgraphviz')' and get the following >> >> > message >> >> > in a pop-up window: >> >> > >> >> > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start >> >> > because >> >> > libcdt-4.dll is missing from your computer. Try reinstalling the >> >> > program >> >> > to >> >> > fix the problem.' >> >> > >> >> > and the following messages within R: >> >> > >> >> > >> >> >> library('Rgraphviz') >> >> > >> >> > Loading required package: graph >> >> > Loading required package: grid >> >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >> >> > ?call: value[[3L]](cond) >> >> > ?error: unable to load shared object 'C:/Users/Mark W >> >> > >> >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >> >> > ?LoadLibrary failure: ?The specified module could not be found. >> >> > >> >> > >> >> > ?Check that (1) graphviz is installed on your system; (2) the >> >> > ?installed version of graphviz matches '2.20.3'; this is the version >> >> > ?used to build this Rgraphviz package; (3) graphviz is accessible to >> >> > ?R, e.g., the path to the graphviz 'bin' directory is in the system >> >> > ?'PATH' variable. ?See additional instructions in the 'README' file >> >> > of >> >> > ?the Rgraphviz 'source' distribution, available at >> >> > >> >> > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> >> > >> >> > ?Ask further questions on the Bioconductor mailing list >> >> > >> >> > ?http://bioconductor.org/docs/mailList.html >> >> > >> >> > >> >> > Error: package/namespace load failed for ?Rgraphviz? >> >> > >> >> >> >> >> > >> >> > >> >> > The file 'C:\Users\Mark W >> >> > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' >> >> > does >> >> > exist in that folder and in the folder where I copied and pasted it >> >> > into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. >> >> > >> >> > >> >> > In addition to the steps described above I have tried countless >> >> > variations >> >> > over approximately 8 hours, including uninstalling R and >> >> > re-installing >> >> > it. >> >> > >> >> > During one reboot maybe 4 hours into this process I even got an error >> >> > message on start-up and almost everything on my desktop had >> >> > disappeared. >> >> > ?I >> >> > restarted the computer again and my normal desktop was restored. ?(I >> >> > found >> >> > a post on the internet describing something similar when trying to >> >> > install >> >> > 'Rgraphviz' but I do not know whether my experience was related to >> >> > that >> >> > previous incident.) >> >> > >> >> > I am hoping someone can provide detailed step-by-step instructions on >> >> > how >> >> > to install the package Rgraphviz and/or identify where I am making a >> >> > mistake based on the information I have provided. ?I have tried to >> >> > include >> >> > here as much information as I can think of. ?If I can include >> >> > additional >> >> > helpful information please let me know. >> >> > >> >> > I wonder whether the above warning message is related to why I cannot >> >> > install 'Rgraphviz': 'Warning message: installed directory not >> >> > writable, >> >> > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', >> >> > 'survival''. >> >> > >> >> >> >> No. That is just biocLite() telling you that those packages couldn't >> >> be updated because they live in a directory that you can't write to. >> >> If you log in as an admin user you can update those packages and make >> >> that message go away, or you can just ignore it. >> >> >> >> Dan >> >> >> >> >> >> > I have not previously posted on this forum. ?Hopefully I am following >> >> > protocol. >> >> > >> >> > Thank you for any advice. >> >> > >> >> > Mark W. Miller >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > > >
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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[cc'ing Bioconductor again] Hi Mark, On Mon, May 28, 2012 at 1:45 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > > Dan, > > Just saw your earlier request for sessioninfo(). > > I have never used that command before, but here is the output when I just > tried it. > > The result when I type: > > C:\>neato -V > > is: > > neato - Graphviz version 2.20.3 (Wed Oct 8 06:02:12 UTC 2008) > > Mark > > > > > R version 2.15.0 (2012-03-30) > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-mingw32/x64 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > ? Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.4.4, ?biocLite for help >> biocLite("Rgraphviz") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Installing package(s) 'Rgraphviz' > trying URL > 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/ 2.15/Rgraphviz_1.34.0.zip' > Content type 'application/zip' length 936601 bytes (914 Kb) > opened URL > downloaded 914 Kb > > package ?Rgraphviz? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > ? ? ? ? C:\Users\Mark W > Miller\AppData\Local\Temp\RtmpyQNH4k\downloaded_packages > Warning message: > installed directory not writable, cannot update packages 'foreign', 'MASS', > ? 'mgcv', 'nlme', 'survival' >> library('Rgraphviz') > Loading required package: graph > Loading required package: grid > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > ? call: value[[3L]](cond) > ? error: unable to load shared object 'C:/Users/Mark W > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': > ? LoadLibrary failure: ?%1 is not a valid Win32 application. > > > ? Check that (1) graphviz is installed on your system; (2) the > ? installed version of graphviz matches '2.20.3'; this is the version > ? used to build this Rgraphviz package; (3) graphviz is accessible to > ? R, e.g., the path to the graphviz 'bin' directory is in the system > ? 'PATH' variable. ?See additional instructions in the 'README' file of > ? the Rgraphviz 'source' distribution, available at > > ? http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html > > ? Ask further questions on the Bioconductor mailing list > > ? http://bioconductor.org/docs/mailList.html > > > Error: package/namespace load failed for ?Rgraphviz? >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United > States.1252 ? ?LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United > States.1252 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > base > > other attached packages: > [1] graph_1.34.0 ? ? ? ?BiocInstaller_1.4.4 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.2.0 stats4_2.15.0 ? ? ?tools_2.15.0 >> > It looks like you are running 64-bit R. Try running 32-bit R by executing: "C:\Program Files\R\R-2.15\bin\i386\R.exe" Does that work? If you don't really need to be running 64-bit R, then just use 32-bit R with Rgraphviz. If you really want to use 64-bit R woth Rgraphviz, install this file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Unzip it in some directory, say c:\graphviz64, then remove the existing graphviz\bin directory from your PATH and add c:\graphviz64\bin. Note that this is not a full version of graphviz, just enough to support Rgraphviz. Dan > > > > > > > > On Mon, May 28, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Mon, May 28, 2012 at 1:36 PM, Mark Miller >> <mark.wayne.miller at="" gmail.com=""> wrote: >> > >> > Thanks, Dan. >> > >> > Unfortunately, that does not solve the problem. >> > >> >> Are you getting the same error message? What is the output of R's >> sessionInfo() >> command? >> >> What happens if you type: >> >> ?neato -V >> >> at a Windows command prompt? >> >> Dan >> >> >> > Mark >> > >> > >> > >> > >> > On Mon, May 28, 2012 at 12:24 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> [cc'ing bioconductor list so others can benefit from this] >> >> >> >> On Mon, May 28, 2012 at 1:16 PM, Mark Miller >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> > >> >> > Hi Dan, >> >> > >> >> > Thank you for the reply. >> >> > >> >> > Below is my current PATH statement: >> >> > >> >> > C:\Program Files\Common Files\Microsoft Shared\Windows >> >> > Live;C:\Program >> >> > Files >> >> > (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program >> >> > Files\Dell\DW >> >> > WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files >> >> > (x86)\AMD >> >> > >> >> > >> >> > APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\Sy stem32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program >> >> > Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program >> >> > Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth >> >> > Software\syswow64;C:\Program Files (x86)\Windows >> >> > Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20 >> >> > >> >> >> >> The directory that should be in your PATH is: >> >> >> >> C:\Program Files (x86)\Graphviz2.20\bin >> >> >> >> (note the \bin at the end). That is where the DLL is located that >> >> Rgraphviz is complaining about, as well as other files it needs. >> >> >> >> >> >> >> >> > You are correct that I had misspelled 'Graphviz' earlier. ?I think I >> >> > have >> >> > spelled it correctly now. ?I tried to check whether that was the >> >> > problem >> >> > by >> >> > first correcting the spelling in the PATH statement and then trying >> >> > to >> >> > re-install Rgraphviz. ?However, I still received errors. >> >> > >> >> > Next I uninstalled Graphviz. ?I noted that I had to manually remove >> >> > Graphviz >> >> > from the PATH statement. ?Then I re-installed Graphviz and added it >> >> > back >> >> > to >> >> > the PATH statement. ?I still receive the pop-up error message >> >> > described >> >> > earlier after re-installing Rgraphviz. >> >> > >> >> > In between uninstalling and re-installing or between correcting, >> >> > removing >> >> > and adding text to the PATH statement I performed frequent reboots >> >> > followed >> >> > by use of the 'echo %PATH%' command statement to check the PATH. >> >> > >> >> >> >> You do not need to reboot your machine after chaning the PATH. You >> >> just need to close and reopen the command prompt window. >> >> >> >> > I think this covers your earlier suggestions. ?Sorry if I overlooked >> >> > any. >> >> > >> >> > I was hoping to install Rgraphviz because I was hoping to explore R's >> >> > ability to act as a GIS system and a reference book on the subject >> >> > used >> >> > Rgraphviz in at least one example file. ?I do not know how frequently >> >> > Rgraphviz is used by that reference, so I do not yet know how >> >> > critical >> >> > Rgraphviz will be for me in pursuing that exploration. >> >> > >> >> > Regardless, thank you for your help. ?Let me know if I can provide >> >> > additional useful information. >> >> > >> >> >> >> If the above suggestions do not help, please send the output of the >> >> sessionInfo() command. I'm wondering if you are running 32- or 64-bit >> >> R. If 64, then you'll need to install a different version of Graphviz. >> >> >> >> Dan >> >> >> >> >> >> > Mark >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> > wrote: >> >> >> >> >> >> Hi Mark, >> >> >> >> >> >> On Sun, May 27, 2012 at 4:13 PM, Mark Miller >> >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> >> > I am attempting to install the package 'Rgraphviz' in R version >> >> >> > 2.15.0 >> >> >> > on a >> >> >> > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). >> >> >> > ?However, >> >> >> > when I type 'library('Rgraphviz')' I keep getting a pop-up error >> >> >> > message >> >> >> > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program >> >> >> > can't >> >> >> > start >> >> >> > because libcdt-4.dll is missing from your computer. Try >> >> >> > reinstalling >> >> >> > the >> >> >> > program to fix the problem.' Within R I get an error message >> >> >> > stating >> >> >> > that >> >> >> > there is no package 'Rgraphviz'. >> >> >> > >> >> >> > I installed Graphviz using a file called 'graphviz-2.20.3.1.msi' >> >> >> > which I >> >> >> > believe I downloaded from the link in an R post found here: >> >> >> > >> >> >> > http://r.789695.n4.nabble.com/Rgraphviz-install- td878526.html >> >> >> > >> >> >> > The actual link within the above R post was: >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://www.graphviz.org/pub/graphviz/stable/windows/graphvi z-2.20.3.1.msi >> >> >> > >> >> >> > >> >> >> > >> >> >> > The directory to Graphviz on my computer is 'c:\Program Files >> >> >> > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in the >> >> >> > folder >> >> >> > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following appears >> >> >> > at >> >> >> > the >> >> >> > end of my path statement 'Program Files (x86)\Graphvis2.20\bin' >> >> >> > and >> >> >> > is >> >> >> > also >> >> >> > displayed when I type 'C:\echo %PATH%' in a command window. >> >> >> > >> >> >> >> >> >> Can you send the full output of the echo %PATH% command? >> >> >> Note that "Graphviz" is mis-spelled above. Could that be the >> >> >> problem? >> >> >> >> >> >> >> >> >> Also note that if you set your PATH in Control Panel, you need to >> >> >> start a new command window after making the change, because the >> >> >> change >> >> >> will not be reflected in any currently open command windows. >> >> >> >> >> >> > The directory to R on my computer is 'c:\Program >> >> >> > Files\R\R-2.15.0\'. >> >> >> > >> >> >> > When I try to install 'Rgraphviz' I get the following messages >> >> >> > within >> >> >> > R: >> >> >> > >> >> >> > >> >> >> >> source("http://bioconductor.org/biocLite.R") >> >> >> > >> >> >> > BiocInstaller version 1.4.4, ?biocLite for help >> >> >> > >> >> >> >> biocLite("Rgraphviz") >> >> >> > >> >> >> > BioC_mirror: http://bioconductor.org >> >> >> > Using R version 2.15, BiocInstaller version 1.4.4. >> >> >> > Installing package(s) 'Rgraphviz' >> >> >> > trying URL ' >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://www.bioconductor.org/packages/2.10/bioc/bin/windows/ contrib/2.15/Rgraphviz_1.34.0.zip >> >> >> > ' >> >> >> > Content type 'application/zip' length 936601 bytes (914 Kb) >> >> >> > opened URL >> >> >> > downloaded 914 Kb >> >> >> > >> >> >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >> >> >> > >> >> >> > The downloaded binary packages are in >> >> >> > ? ? ? ?C:\Users\Mark W >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages >> >> >> > Warning message: >> >> >> > installed directory not writable, cannot update packages >> >> >> > 'foreign', >> >> >> > 'MASS', >> >> >> > ?'mgcv', 'nlme', 'survival' >> >> >> > >> >> >> >> >> >> >> > >> >> >> > >> >> >> > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and the >> >> >> > package >> >> >> > 'Rgraphviz' does not appear in the R library in 'c:\Program >> >> >> > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in >> >> >> > 'C:\users\Mark >> >> >> > W >> >> >> > Miller\Documents\R\win-library\2.15' >> >> >> > >> >> >> >> >> >> This is ok. >> >> >> >> >> >> >> >> >> > I have copied and pasted the 'Rgraphviz' folder from >> >> >> > 'C:\users\Mark W >> >> >> > Miller\Documents\R\win-library\2.15' into 'C:\Program >> >> >> > Files\R\R-2.15.0\library\'. >> >> >> >> >> >> >> >> >> You do not need to do this. >> >> >> >> >> >> > >> >> >> > Then inside R I type 'library('Rgraphviz')' and get the following >> >> >> > message >> >> >> > in a pop-up window: >> >> >> > >> >> >> > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't start >> >> >> > because >> >> >> > libcdt-4.dll is missing from your computer. Try reinstalling the >> >> >> > program >> >> >> > to >> >> >> > fix the problem.' >> >> >> > >> >> >> > and the following messages within R: >> >> >> > >> >> >> > >> >> >> >> library('Rgraphviz') >> >> >> > >> >> >> > Loading required package: graph >> >> >> > Loading required package: grid >> >> >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', >> >> >> > details: >> >> >> > ?call: value[[3L]](cond) >> >> >> > ?error: unable to load shared object 'C:/Users/Mark W >> >> >> > >> >> >> > >> >> >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >> >> >> > ?LoadLibrary failure: ?The specified module could not be found. >> >> >> > >> >> >> > >> >> >> > ?Check that (1) graphviz is installed on your system; (2) the >> >> >> > ?installed version of graphviz matches '2.20.3'; this is the >> >> >> > version >> >> >> > ?used to build this Rgraphviz package; (3) graphviz is accessible >> >> >> > to >> >> >> > ?R, e.g., the path to the graphviz 'bin' directory is in the >> >> >> > system >> >> >> > ?'PATH' variable. ?See additional instructions in the 'README' >> >> >> > file >> >> >> > of >> >> >> > ?the Rgraphviz 'source' distribution, available at >> >> >> > >> >> >> > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> >> >> > >> >> >> > ?Ask further questions on the Bioconductor mailing list >> >> >> > >> >> >> > ?http://bioconductor.org/docs/mailList.html >> >> >> > >> >> >> > >> >> >> > Error: package/namespace load failed for ?Rgraphviz? >> >> >> > >> >> >> >> >> >> >> > >> >> >> > >> >> >> > The file 'C:\Users\Mark W >> >> >> > >> >> >> > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' >> >> >> > does >> >> >> > exist in that folder and in the folder where I copied and pasted >> >> >> > it >> >> >> > into: 'c:\Program Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. >> >> >> > >> >> >> > >> >> >> > In addition to the steps described above I have tried countless >> >> >> > variations >> >> >> > over approximately 8 hours, including uninstalling R and >> >> >> > re-installing >> >> >> > it. >> >> >> > >> >> >> > During one reboot maybe 4 hours into this process I even got an >> >> >> > error >> >> >> > message on start-up and almost everything on my desktop had >> >> >> > disappeared. >> >> >> > ?I >> >> >> > restarted the computer again and my normal desktop was restored. >> >> >> > ?(I >> >> >> > found >> >> >> > a post on the internet describing something similar when trying to >> >> >> > install >> >> >> > 'Rgraphviz' but I do not know whether my experience was related to >> >> >> > that >> >> >> > previous incident.) >> >> >> > >> >> >> > I am hoping someone can provide detailed step-by-step instructions >> >> >> > on >> >> >> > how >> >> >> > to install the package Rgraphviz and/or identify where I am making >> >> >> > a >> >> >> > mistake based on the information I have provided. ?I have tried to >> >> >> > include >> >> >> > here as much information as I can think of. ?If I can include >> >> >> > additional >> >> >> > helpful information please let me know. >> >> >> > >> >> >> > I wonder whether the above warning message is related to why I >> >> >> > cannot >> >> >> > install 'Rgraphviz': 'Warning message: installed directory not >> >> >> > writable, >> >> >> > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', >> >> >> > 'survival''. >> >> >> > >> >> >> >> >> >> No. That is just biocLite() telling you that those packages couldn't >> >> >> be updated because they live in a directory that you can't write to. >> >> >> If you log in as an admin user you can update those packages and >> >> >> make >> >> >> that message go away, or you can just ignore it. >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> > I have not previously posted on this forum. ?Hopefully I am >> >> >> > following >> >> >> > protocol. >> >> >> > >> >> >> > Thank you for any advice. >> >> >> > >> >> >> > Mark W. Miller >> >> >> > >> >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> >> > >> >> >> > >> >> >> > _______________________________________________ >> >> >> > Bioconductor mailing list >> >> >> > Bioconductor at r-project.org >> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> > Search the archives: >> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> > >> > >> > > >
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States
On Mon, May 28, 2012 at 2:09 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > > Hi Dan, > > When I click on "C:\Program Files\R\R-2.15\bin\i386\R.exe" R opens in a > command window as a command-line program. ?I have never used R that way. > > When I installed R I think it installs both 32-bit and 64-bit versions and > places desktop icons for both versions. ?I just remove the desktop icon for > the 32-bit version. ?Would it be okay if I re-install R and try running the > 32-bit version from the desktop icon? ?Do you think Rgraphviz would work > that way? ?Or must the 32-bit version of R operate from a command window for > Rgraphviz to function? > > I am sure the 32-bit version is still installed on my machine. ?I just do > not know how to open the GUI I am used to without the desktop icon present > given that clicking on R.exe above opened a command window. > Try: C:\Program Files\R\R-2.15\bin\i386\Rgui.exe Now try library(Rgraphviz) Does it work? You don't need to reinstall R. Just right click on Rgui.exe and make a desktop shortcut, an use that to access R from now on. Dan > Mark > > > > On Mon, May 28, 2012 at 12:54 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> [cc'ing Bioconductor again] >> >> Hi Mark, >> >> On Mon, May 28, 2012 at 1:45 PM, Mark Miller >> <mark.wayne.miller at="" gmail.com=""> wrote: >> > >> > Dan, >> > >> > Just saw your earlier request for sessioninfo(). >> > >> > I have never used that command before, but here is the output when I >> > just >> > tried it. >> > >> > The result when I type: >> > >> > C:\>neato -V >> > >> > is: >> > >> > neato - Graphviz version 2.20.3 (Wed Oct 8 06:02:12 UTC 2008) >> > >> > Mark >> > >> > >> > >> > >> > R version 2.15.0 (2012-03-30) >> > Copyright (C) 2012 The R Foundation for Statistical Computing >> > ISBN 3-900051-07-0 >> > Platform: x86_64-pc-mingw32/x64 (64-bit) >> > >> > R is free software and comes with ABSOLUTELY NO WARRANTY. >> > You are welcome to redistribute it under certain conditions. >> > Type 'license()' or 'licence()' for distribution details. >> > >> > ? Natural language support but running in an English locale >> > >> > R is a collaborative project with many contributors. >> > Type 'contributors()' for more information and >> > 'citation()' on how to cite R or R packages in publications. >> > >> > Type 'demo()' for some demos, 'help()' for on-line help, or >> > 'help.start()' for an HTML browser interface to help. >> > Type 'q()' to quit R. >> > >> >> source("http://bioconductor.org/biocLite.R") >> > BiocInstaller version 1.4.4, ?biocLite for help >> >> biocLite("Rgraphviz") >> > BioC_mirror: http://bioconductor.org >> > Using R version 2.15, BiocInstaller version 1.4.4. >> > Installing package(s) 'Rgraphviz' >> > trying URL >> > >> > 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contr ib/2.15/Rgraphviz_1.34.0.zip' >> > Content type 'application/zip' length 936601 bytes (914 Kb) >> > opened URL >> > downloaded 914 Kb >> > >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >> > >> > The downloaded binary packages are in >> > ? ? ? ? C:\Users\Mark W >> > Miller\AppData\Local\Temp\RtmpyQNH4k\downloaded_packages >> > Warning message: >> > installed directory not writable, cannot update packages 'foreign', >> > 'MASS', >> > ? 'mgcv', 'nlme', 'survival' >> >> library('Rgraphviz') >> > Loading required package: graph >> > Loading required package: grid >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >> > ? call: value[[3L]](cond) >> > ? error: unable to load shared object 'C:/Users/Mark W >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >> > ? LoadLibrary failure: ?%1 is not a valid Win32 application. >> > >> > >> > ? Check that (1) graphviz is installed on your system; (2) the >> > ? installed version of graphviz matches '2.20.3'; this is the version >> > ? used to build this Rgraphviz package; (3) graphviz is accessible to >> > ? R, e.g., the path to the graphviz 'bin' directory is in the system >> > ? 'PATH' variable. ?See additional instructions in the 'README' file of >> > ? the Rgraphviz 'source' distribution, available at >> > >> > ? http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> > >> > ? Ask further questions on the Bioconductor mailing list >> > >> > ? http://bioconductor.org/docs/mailList.html >> > >> > >> > Error: package/namespace load failed for ?Rgraphviz? >> >> sessionInfo() >> > R version 2.15.0 (2012-03-30) >> > Platform: x86_64-pc-mingw32/x64 (64-bit) >> > >> > locale: >> > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >> > States.1252 ? ?LC_MONETARY=English_United States.1252 >> > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United >> > States.1252 >> > >> > attached base packages: >> > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> > base >> > >> > other attached packages: >> > [1] graph_1.34.0 ? ? ? ?BiocInstaller_1.4.4 >> > >> > loaded via a namespace (and not attached): >> > [1] BiocGenerics_0.2.0 stats4_2.15.0 ? ? ?tools_2.15.0 >> >> >> > >> >> >> It looks like you are running 64-bit R. Try running 32-bit R by executing: >> >> "C:\Program Files\R\R-2.15\bin\i386\R.exe" >> >> Does that work? >> >> If you don't really need to be running 64-bit R, then just use 32-bit >> R with Rgraphviz. >> If you really want to use 64-bit R woth Rgraphviz, install this file: >> >> http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip >> >> Unzip it in some directory, say c:\graphviz64, then remove the >> existing graphviz\bin directory from your PATH and add >> c:\graphviz64\bin. Note that this is not a full version of graphviz, >> just enough to support Rgraphviz. >> >> Dan >> >> >> >> > >> > >> > >> > >> > >> > >> > >> > On Mon, May 28, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> On Mon, May 28, 2012 at 1:36 PM, Mark Miller >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> > >> >> > Thanks, Dan. >> >> > >> >> > Unfortunately, that does not solve the problem. >> >> > >> >> >> >> Are you getting the same error message? What is the output of R's >> >> sessionInfo() >> >> command? >> >> >> >> What happens if you type: >> >> >> >> ?neato -V >> >> >> >> at a Windows command prompt? >> >> >> >> Dan >> >> >> >> >> >> > Mark >> >> > >> >> > >> >> > >> >> > >> >> > On Mon, May 28, 2012 at 12:24 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> > wrote: >> >> >> >> >> >> [cc'ing bioconductor list so others can benefit from this] >> >> >> >> >> >> On Mon, May 28, 2012 at 1:16 PM, Mark Miller >> >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> >> > >> >> >> > Hi Dan, >> >> >> > >> >> >> > Thank you for the reply. >> >> >> > >> >> >> > Below is my current PATH statement: >> >> >> > >> >> >> > C:\Program Files\Common Files\Microsoft Shared\Windows >> >> >> > Live;C:\Program >> >> >> > Files >> >> >> > (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program >> >> >> > Files\Dell\DW >> >> >> > WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program >> >> >> > Files >> >> >> > (x86)\AMD >> >> >> > >> >> >> > >> >> >> > >> >> >> > APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot% \System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Progra m >> >> >> > Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program >> >> >> > Files\WIDCOMM\Bluetooth Software\;C:\Program >> >> >> > Files\WIDCOMM\Bluetooth >> >> >> > Software\syswow64;C:\Program Files (x86)\Windows >> >> >> > Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20 >> >> >> > >> >> >> >> >> >> The directory that should be in your PATH is: >> >> >> >> >> >> C:\Program Files (x86)\Graphviz2.20\bin >> >> >> >> >> >> (note the \bin at the end). That is where the DLL is located that >> >> >> Rgraphviz is complaining about, as well as other files it needs. >> >> >> >> >> >> >> >> >> >> >> >> > You are correct that I had misspelled 'Graphviz' earlier. ?I think >> >> >> > I >> >> >> > have >> >> >> > spelled it correctly now. ?I tried to check whether that was the >> >> >> > problem >> >> >> > by >> >> >> > first correcting the spelling in the PATH statement and then >> >> >> > trying >> >> >> > to >> >> >> > re-install Rgraphviz. ?However, I still received errors. >> >> >> > >> >> >> > Next I uninstalled Graphviz. ?I noted that I had to manually >> >> >> > remove >> >> >> > Graphviz >> >> >> > from the PATH statement. ?Then I re-installed Graphviz and added >> >> >> > it >> >> >> > back >> >> >> > to >> >> >> > the PATH statement. ?I still receive the pop-up error message >> >> >> > described >> >> >> > earlier after re-installing Rgraphviz. >> >> >> > >> >> >> > In between uninstalling and re-installing or between correcting, >> >> >> > removing >> >> >> > and adding text to the PATH statement I performed frequent reboots >> >> >> > followed >> >> >> > by use of the 'echo %PATH%' command statement to check the PATH. >> >> >> > >> >> >> >> >> >> You do not need to reboot your machine after chaning the PATH. You >> >> >> just need to close and reopen the command prompt window. >> >> >> >> >> >> > I think this covers your earlier suggestions. ?Sorry if I >> >> >> > overlooked >> >> >> > any. >> >> >> > >> >> >> > I was hoping to install Rgraphviz because I was hoping to explore >> >> >> > R's >> >> >> > ability to act as a GIS system and a reference book on the subject >> >> >> > used >> >> >> > Rgraphviz in at least one example file. ?I do not know how >> >> >> > frequently >> >> >> > Rgraphviz is used by that reference, so I do not yet know how >> >> >> > critical >> >> >> > Rgraphviz will be for me in pursuing that exploration. >> >> >> > >> >> >> > Regardless, thank you for your help. ?Let me know if I can provide >> >> >> > additional useful information. >> >> >> > >> >> >> >> >> >> If the above suggestions do not help, please send the output of the >> >> >> sessionInfo() command. I'm wondering if you are running 32- or >> >> >> 64-bit >> >> >> R. If 64, then you'll need to install a different version of >> >> >> Graphviz. >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> > Mark >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum >> >> >> > <dtenenba at="" fhcrc.org=""> >> >> >> > wrote: >> >> >> >> >> >> >> >> Hi Mark, >> >> >> >> >> >> >> >> On Sun, May 27, 2012 at 4:13 PM, Mark Miller >> >> >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >> >> >> >> > I am attempting to install the package 'Rgraphviz' in R version >> >> >> >> > 2.15.0 >> >> >> >> > on a >> >> >> >> > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 (64-bit). >> >> >> >> > ?However, >> >> >> >> > when I type 'library('Rgraphviz')' I keep getting a pop- up >> >> >> >> > error >> >> >> >> > message >> >> >> >> > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program >> >> >> >> > can't >> >> >> >> > start >> >> >> >> > because libcdt-4.dll is missing from your computer. Try >> >> >> >> > reinstalling >> >> >> >> > the >> >> >> >> > program to fix the problem.' Within R I get an error message >> >> >> >> > stating >> >> >> >> > that >> >> >> >> > there is no package 'Rgraphviz'. >> >> >> >> > >> >> >> >> > I installed Graphviz using a file called >> >> >> >> > 'graphviz-2.20.3.1.msi' >> >> >> >> > which I >> >> >> >> > believe I downloaded from the link in an R post found here: >> >> >> >> > >> >> >> >> > http://r.789695.n4.nabble.com/Rgraphviz-install- td878526.html >> >> >> >> > >> >> >> >> > The actual link within the above R post was: >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > http://www.graphviz.org/pub/graphviz/stable/windows/grap hviz-2.20.3.1.msi >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > The directory to Graphviz on my computer is 'c:\Program Files >> >> >> >> > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in >> >> >> >> > the >> >> >> >> > folder >> >> >> >> > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following >> >> >> >> > appears >> >> >> >> > at >> >> >> >> > the >> >> >> >> > end of my path statement 'Program Files (x86)\Graphvis2.20\bin' >> >> >> >> > and >> >> >> >> > is >> >> >> >> > also >> >> >> >> > displayed when I type 'C:\echo %PATH%' in a command window. >> >> >> >> > >> >> >> >> >> >> >> >> Can you send the full output of the echo %PATH% command? >> >> >> >> Note that "Graphviz" is mis-spelled above. Could that be the >> >> >> >> problem? >> >> >> >> >> >> >> >> >> >> >> >> Also note that if you set your PATH in Control Panel, you need to >> >> >> >> start a new command window after making the change, because the >> >> >> >> change >> >> >> >> will not be reflected in any currently open command windows. >> >> >> >> >> >> >> >> > The directory to R on my computer is 'c:\Program >> >> >> >> > Files\R\R-2.15.0\'. >> >> >> >> > >> >> >> >> > When I try to install 'Rgraphviz' I get the following messages >> >> >> >> > within >> >> >> >> > R: >> >> >> >> > >> >> >> >> > >> >> >> >> >> source("http://bioconductor.org/biocLite.R") >> >> >> >> > >> >> >> >> > BiocInstaller version 1.4.4, ?biocLite for help >> >> >> >> > >> >> >> >> >> biocLite("Rgraphviz") >> >> >> >> > >> >> >> >> > BioC_mirror: http://bioconductor.org >> >> >> >> > Using R version 2.15, BiocInstaller version 1.4.4. >> >> >> >> > Installing package(s) 'Rgraphviz' >> >> >> >> > trying URL ' >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > http://www.bioconductor.org/packages/2.10/bioc/bin/windo ws/contrib/2.15/Rgraphviz_1.34.0.zip >> >> >> >> > ' >> >> >> >> > Content type 'application/zip' length 936601 bytes (914 Kb) >> >> >> >> > opened URL >> >> >> >> > downloaded 914 Kb >> >> >> >> > >> >> >> >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >> >> >> >> > >> >> >> >> > The downloaded binary packages are in >> >> >> >> > ? ? ? ?C:\Users\Mark W >> >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages >> >> >> >> > Warning message: >> >> >> >> > installed directory not writable, cannot update packages >> >> >> >> > 'foreign', >> >> >> >> > 'MASS', >> >> >> >> > ?'mgcv', 'nlme', 'survival' >> >> >> >> > >> >> >> >> >> >> >> >> >> > >> >> >> >> > >> >> >> >> > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W >> >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and >> >> >> >> > the >> >> >> >> > package >> >> >> >> > 'Rgraphviz' does not appear in the R library in 'c:\Program >> >> >> >> > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in >> >> >> >> > 'C:\users\Mark >> >> >> >> > W >> >> >> >> > Miller\Documents\R\win-library\2.15' >> >> >> >> > >> >> >> >> >> >> >> >> This is ok. >> >> >> >> >> >> >> >> >> >> >> >> > I have copied and pasted the 'Rgraphviz' folder from >> >> >> >> > 'C:\users\Mark W >> >> >> >> > Miller\Documents\R\win-library\2.15' into 'C:\Program >> >> >> >> > Files\R\R-2.15.0\library\'. >> >> >> >> >> >> >> >> >> >> >> >> You do not need to do this. >> >> >> >> >> >> >> >> > >> >> >> >> > Then inside R I type 'library('Rgraphviz')' and get the >> >> >> >> > following >> >> >> >> > message >> >> >> >> > in a pop-up window: >> >> >> >> > >> >> >> >> > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't >> >> >> >> > start >> >> >> >> > because >> >> >> >> > libcdt-4.dll is missing from your computer. Try reinstalling >> >> >> >> > the >> >> >> >> > program >> >> >> >> > to >> >> >> >> > fix the problem.' >> >> >> >> > >> >> >> >> > and the following messages within R: >> >> >> >> > >> >> >> >> > >> >> >> >> >> library('Rgraphviz') >> >> >> >> > >> >> >> >> > Loading required package: graph >> >> >> >> > Loading required package: grid >> >> >> >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', >> >> >> >> > details: >> >> >> >> > ?call: value[[3L]](cond) >> >> >> >> > ?error: unable to load shared object 'C:/Users/Mark W >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >> >> >> >> > ?LoadLibrary failure: ?The specified module could not be found. >> >> >> >> > >> >> >> >> > >> >> >> >> > ?Check that (1) graphviz is installed on your system; (2) the >> >> >> >> > ?installed version of graphviz matches '2.20.3'; this is the >> >> >> >> > version >> >> >> >> > ?used to build this Rgraphviz package; (3) graphviz is >> >> >> >> > accessible >> >> >> >> > to >> >> >> >> > ?R, e.g., the path to the graphviz 'bin' directory is in the >> >> >> >> > system >> >> >> >> > ?'PATH' variable. ?See additional instructions in the 'README' >> >> >> >> > file >> >> >> >> > of >> >> >> >> > ?the Rgraphviz 'source' distribution, available at >> >> >> >> > >> >> >> >> > >> >> >> >> > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> >> >> >> > >> >> >> >> > ?Ask further questions on the Bioconductor mailing list >> >> >> >> > >> >> >> >> > ?http://bioconductor.org/docs/mailList.html >> >> >> >> > >> >> >> >> > >> >> >> >> > Error: package/namespace load failed for ?Rgraphviz? >> >> >> >> > >> >> >> >> >> >> >> >> >> > >> >> >> >> > >> >> >> >> > The file 'C:\Users\Mark W >> >> >> >> > >> >> >> >> > >> >> >> >> > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' >> >> >> >> > does >> >> >> >> > exist in that folder and in the folder where I copied and >> >> >> >> > pasted >> >> >> >> > it >> >> >> >> > into: 'c:\Program >> >> >> >> > Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. >> >> >> >> > >> >> >> >> > >> >> >> >> > In addition to the steps described above I have tried countless >> >> >> >> > variations >> >> >> >> > over approximately 8 hours, including uninstalling R and >> >> >> >> > re-installing >> >> >> >> > it. >> >> >> >> > >> >> >> >> > During one reboot maybe 4 hours into this process I even got an >> >> >> >> > error >> >> >> >> > message on start-up and almost everything on my desktop had >> >> >> >> > disappeared. >> >> >> >> > ?I >> >> >> >> > restarted the computer again and my normal desktop was >> >> >> >> > restored. >> >> >> >> > ?(I >> >> >> >> > found >> >> >> >> > a post on the internet describing something similar when trying >> >> >> >> > to >> >> >> >> > install >> >> >> >> > 'Rgraphviz' but I do not know whether my experience was related >> >> >> >> > to >> >> >> >> > that >> >> >> >> > previous incident.) >> >> >> >> > >> >> >> >> > I am hoping someone can provide detailed step-by-step >> >> >> >> > instructions >> >> >> >> > on >> >> >> >> > how >> >> >> >> > to install the package Rgraphviz and/or identify where I am >> >> >> >> > making >> >> >> >> > a >> >> >> >> > mistake based on the information I have provided. ?I have tried >> >> >> >> > to >> >> >> >> > include >> >> >> >> > here as much information as I can think of. ?If I can include >> >> >> >> > additional >> >> >> >> > helpful information please let me know. >> >> >> >> > >> >> >> >> > I wonder whether the above warning message is related to why I >> >> >> >> > cannot >> >> >> >> > install 'Rgraphviz': 'Warning message: installed directory not >> >> >> >> > writable, >> >> >> >> > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', >> >> >> >> > 'survival''. >> >> >> >> > >> >> >> >> >> >> >> >> No. That is just biocLite() telling you that those packages >> >> >> >> couldn't >> >> >> >> be updated because they live in a directory that you can't write >> >> >> >> to. >> >> >> >> If you log in as an admin user you can update those packages and >> >> >> >> make >> >> >> >> that message go away, or you can just ignore it. >> >> >> >> >> >> >> >> Dan >> >> >> >> >> >> >> >> >> >> >> >> > I have not previously posted on this forum. ?Hopefully I am >> >> >> >> > following >> >> >> >> > protocol. >> >> >> >> > >> >> >> >> > Thank you for any advice. >> >> >> >> > >> >> >> >> > Mark W. Miller >> >> >> >> > >> >> >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> >> >> > >> >> >> >> > >> >> >> >> > _______________________________________________ >> >> >> >> > Bioconductor mailing list >> >> >> >> > Bioconductor at r-project.org >> >> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > Search the archives: >> >> >> >> > >> >> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > >> >> >> > >> >> > >> >> > >> > >> > > >
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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On Mon, May 28, 2012 at 2:13 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> wrote: > > Dan, > > I found the *.exe file needed to open the 32-bit version of R and was able > to install 'Rgraphviz'! > > Thanks for your help with this. ?I hope this helps others. > Glad it works. Dan > Mark > > > > On Mon, May 28, 2012 at 1:09 PM, Mark Miller <mark.wayne.miller at="" gmail.com=""> > wrote: >> >> >> Hi Dan, >> >> When I click on "C:\Program Files\R\R-2.15\bin\i386\R.exe" R opens in a >> command window as a command-line program. ?I have never used R that way. >> >> When I installed R I think it installs both 32-bit and 64-bit versions and >> places desktop icons for both versions. ?I just remove the desktop icon for >> the 32-bit version. ?Would it be okay if I re-install R and try running the >> 32-bit version from the desktop icon? ?Do you think Rgraphviz would work >> that way? ?Or must the 32-bit version of R operate from a command window for >> Rgraphviz to function? >> >> I am sure the 32-bit version is still installed on my machine. ?I just do >> not know how to open the GUI I am used to without the desktop icon present >> given that clicking on R.exe above opened a command window. >> >> Mark >> >> >> >> On Mon, May 28, 2012 at 12:54 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >>> >>> [cc'ing Bioconductor again] >>> >>> Hi Mark, >>> >>> On Mon, May 28, 2012 at 1:45 PM, Mark Miller >>> <mark.wayne.miller at="" gmail.com=""> wrote: >>> > >>> > Dan, >>> > >>> > Just saw your earlier request for sessioninfo(). >>> > >>> > I have never used that command before, but here is the output when I >>> > just >>> > tried it. >>> > >>> > The result when I type: >>> > >>> > C:\>neato -V >>> > >>> > is: >>> > >>> > neato - Graphviz version 2.20.3 (Wed Oct 8 06:02:12 UTC 2008) >>> > >>> > Mark >>> > >>> > >>> > >>> > >>> > R version 2.15.0 (2012-03-30) >>> > Copyright (C) 2012 The R Foundation for Statistical Computing >>> > ISBN 3-900051-07-0 >>> > Platform: x86_64-pc-mingw32/x64 (64-bit) >>> > >>> > R is free software and comes with ABSOLUTELY NO WARRANTY. >>> > You are welcome to redistribute it under certain conditions. >>> > Type 'license()' or 'licence()' for distribution details. >>> > >>> > ? Natural language support but running in an English locale >>> > >>> > R is a collaborative project with many contributors. >>> > Type 'contributors()' for more information and >>> > 'citation()' on how to cite R or R packages in publications. >>> > >>> > Type 'demo()' for some demos, 'help()' for on-line help, or >>> > 'help.start()' for an HTML browser interface to help. >>> > Type 'q()' to quit R. >>> > >>> >> source("http://bioconductor.org/biocLite.R") >>> > BiocInstaller version 1.4.4, ?biocLite for help >>> >> biocLite("Rgraphviz") >>> > BioC_mirror: http://bioconductor.org >>> > Using R version 2.15, BiocInstaller version 1.4.4. >>> > Installing package(s) 'Rgraphviz' >>> > trying URL >>> > >>> > 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/cont rib/2.15/Rgraphviz_1.34.0.zip' >>> > Content type 'application/zip' length 936601 bytes (914 Kb) >>> > opened URL >>> > downloaded 914 Kb >>> > >>> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >>> > >>> > The downloaded binary packages are in >>> > ? ? ? ? C:\Users\Mark W >>> > Miller\AppData\Local\Temp\RtmpyQNH4k\downloaded_packages >>> > Warning message: >>> > installed directory not writable, cannot update packages 'foreign', >>> > 'MASS', >>> > ? 'mgcv', 'nlme', 'survival' >>> >> library('Rgraphviz') >>> > Loading required package: graph >>> > Loading required package: grid >>> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >>> > ? call: value[[3L]](cond) >>> > ? error: unable to load shared object 'C:/Users/Mark W >>> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >>> > ? LoadLibrary failure: ?%1 is not a valid Win32 application. >>> > >>> > >>> > ? Check that (1) graphviz is installed on your system; (2) the >>> > ? installed version of graphviz matches '2.20.3'; this is the version >>> > ? used to build this Rgraphviz package; (3) graphviz is accessible to >>> > ? R, e.g., the path to the graphviz 'bin' directory is in the system >>> > ? 'PATH' variable. ?See additional instructions in the 'README' file of >>> > ? the Rgraphviz 'source' distribution, available at >>> > >>> > ? http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >>> > >>> > ? Ask further questions on the Bioconductor mailing list >>> > >>> > ? http://bioconductor.org/docs/mailList.html >>> > >>> > >>> > Error: package/namespace load failed for ?Rgraphviz? >>> >> sessionInfo() >>> > R version 2.15.0 (2012-03-30) >>> > Platform: x86_64-pc-mingw32/x64 (64-bit) >>> > >>> > locale: >>> > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United >>> > States.1252 ? ?LC_MONETARY=English_United States.1252 >>> > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United >>> > States.1252 >>> > >>> > attached base packages: >>> > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods >>> > base >>> > >>> > other attached packages: >>> > [1] graph_1.34.0 ? ? ? ?BiocInstaller_1.4.4 >>> > >>> > loaded via a namespace (and not attached): >>> > [1] BiocGenerics_0.2.0 stats4_2.15.0 ? ? ?tools_2.15.0 >>> >> >>> > >>> >>> >>> It looks like you are running 64-bit R. Try running 32-bit R by >>> executing: >>> >>> "C:\Program Files\R\R-2.15\bin\i386\R.exe" >>> >>> Does that work? >>> >>> If you don't really need to be running 64-bit R, then just use 32-bit >>> R with Rgraphviz. >>> If you really want to use 64-bit R woth Rgraphviz, install this file: >>> >>> http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip >>> >>> Unzip it in some directory, say c:\graphviz64, then remove the >>> existing graphviz\bin directory from your PATH and add >>> c:\graphviz64\bin. Note that this is not a full version of graphviz, >>> just enough to support Rgraphviz. >>> >>> Dan >>> >>> >>> >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > On Mon, May 28, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> > wrote: >>> >> >>> >> On Mon, May 28, 2012 at 1:36 PM, Mark Miller >>> >> <mark.wayne.miller at="" gmail.com=""> wrote: >>> >> > >>> >> > Thanks, Dan. >>> >> > >>> >> > Unfortunately, that does not solve the problem. >>> >> > >>> >> >>> >> Are you getting the same error message? What is the output of R's >>> >> sessionInfo() >>> >> command? >>> >> >>> >> What happens if you type: >>> >> >>> >> ?neato -V >>> >> >>> >> at a Windows command prompt? >>> >> >>> >> Dan >>> >> >>> >> >>> >> > Mark >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > On Mon, May 28, 2012 at 12:24 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> >> > wrote: >>> >> >> >>> >> >> [cc'ing bioconductor list so others can benefit from this] >>> >> >> >>> >> >> On Mon, May 28, 2012 at 1:16 PM, Mark Miller >>> >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >>> >> >> > >>> >> >> > Hi Dan, >>> >> >> > >>> >> >> > Thank you for the reply. >>> >> >> > >>> >> >> > Below is my current PATH statement: >>> >> >> > >>> >> >> > C:\Program Files\Common Files\Microsoft Shared\Windows >>> >> >> > Live;C:\Program >>> >> >> > Files >>> >> >> > (x86)\Common Files\Microsoft Shared\Windows Live;C:\Program >>> >> >> > Files\Dell\DW >>> >> >> > WLAN Card;;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program >>> >> >> > Files >>> >> >> > (x86)\AMD >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > APP\bin\x86;%SystemRoot%\system32;%SystemRoot%;%SystemRoot %\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Progr am >>> >> >> > Files (x86)\ATI Technologies\ATI.ACE\Core- Static;C:\Program >>> >> >> > Files\WIDCOMM\Bluetooth Software\;C:\Program >>> >> >> > Files\WIDCOMM\Bluetooth >>> >> >> > Software\syswow64;C:\Program Files (x86)\Windows >>> >> >> > Live\Shared;c:\MinGW\bin;C:\Program Files (x86)\Graphviz2.20 >>> >> >> > >>> >> >> >>> >> >> The directory that should be in your PATH is: >>> >> >> >>> >> >> C:\Program Files (x86)\Graphviz2.20\bin >>> >> >> >>> >> >> (note the \bin at the end). That is where the DLL is located that >>> >> >> Rgraphviz is complaining about, as well as other files it needs. >>> >> >> >>> >> >> >>> >> >> >>> >> >> > You are correct that I had misspelled 'Graphviz' earlier. ?I >>> >> >> > think I >>> >> >> > have >>> >> >> > spelled it correctly now. ?I tried to check whether that was the >>> >> >> > problem >>> >> >> > by >>> >> >> > first correcting the spelling in the PATH statement and then >>> >> >> > trying >>> >> >> > to >>> >> >> > re-install Rgraphviz. ?However, I still received errors. >>> >> >> > >>> >> >> > Next I uninstalled Graphviz. ?I noted that I had to manually >>> >> >> > remove >>> >> >> > Graphviz >>> >> >> > from the PATH statement. ?Then I re-installed Graphviz and added >>> >> >> > it >>> >> >> > back >>> >> >> > to >>> >> >> > the PATH statement. ?I still receive the pop-up error message >>> >> >> > described >>> >> >> > earlier after re-installing Rgraphviz. >>> >> >> > >>> >> >> > In between uninstalling and re-installing or between correcting, >>> >> >> > removing >>> >> >> > and adding text to the PATH statement I performed frequent >>> >> >> > reboots >>> >> >> > followed >>> >> >> > by use of the 'echo %PATH%' command statement to check the PATH. >>> >> >> > >>> >> >> >>> >> >> You do not need to reboot your machine after chaning the PATH. You >>> >> >> just need to close and reopen the command prompt window. >>> >> >> >>> >> >> > I think this covers your earlier suggestions. ?Sorry if I >>> >> >> > overlooked >>> >> >> > any. >>> >> >> > >>> >> >> > I was hoping to install Rgraphviz because I was hoping to explore >>> >> >> > R's >>> >> >> > ability to act as a GIS system and a reference book on the >>> >> >> > subject >>> >> >> > used >>> >> >> > Rgraphviz in at least one example file. ?I do not know how >>> >> >> > frequently >>> >> >> > Rgraphviz is used by that reference, so I do not yet know how >>> >> >> > critical >>> >> >> > Rgraphviz will be for me in pursuing that exploration. >>> >> >> > >>> >> >> > Regardless, thank you for your help. ?Let me know if I can >>> >> >> > provide >>> >> >> > additional useful information. >>> >> >> > >>> >> >> >>> >> >> If the above suggestions do not help, please send the output of the >>> >> >> sessionInfo() command. I'm wondering if you are running 32- or >>> >> >> 64-bit >>> >> >> R. If 64, then you'll need to install a different version of >>> >> >> Graphviz. >>> >> >> >>> >> >> Dan >>> >> >> >>> >> >> >>> >> >> > Mark >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > On Mon, May 28, 2012 at 9:35 AM, Dan Tenenbaum >>> >> >> > <dtenenba at="" fhcrc.org=""> >>> >> >> > wrote: >>> >> >> >> >>> >> >> >> Hi Mark, >>> >> >> >> >>> >> >> >> On Sun, May 27, 2012 at 4:13 PM, Mark Miller >>> >> >> >> <mark.wayne.miller at="" gmail.com=""> wrote: >>> >> >> >> > I am attempting to install the package 'Rgraphviz' in R >>> >> >> >> > version >>> >> >> >> > 2.15.0 >>> >> >> >> > on a >>> >> >> >> > PC running Windows 7, Platform: x86_64-pc-mingw32/x64 >>> >> >> >> > (64-bit). >>> >> >> >> > ?However, >>> >> >> >> > when I type 'library('Rgraphviz')' I keep getting a pop-up >>> >> >> >> > error >>> >> >> >> > message >>> >> >> >> > stating 'DP_LocalAvatar: Rgui.exe - System Error' 'The program >>> >> >> >> > can't >>> >> >> >> > start >>> >> >> >> > because libcdt-4.dll is missing from your computer. Try >>> >> >> >> > reinstalling >>> >> >> >> > the >>> >> >> >> > program to fix the problem.' Within R I get an error message >>> >> >> >> > stating >>> >> >> >> > that >>> >> >> >> > there is no package 'Rgraphviz'. >>> >> >> >> > >>> >> >> >> > I installed Graphviz using a file called >>> >> >> >> > 'graphviz-2.20.3.1.msi' >>> >> >> >> > which I >>> >> >> >> > believe I downloaded from the link in an R post found here: >>> >> >> >> > >>> >> >> >> > http://r.789695.n4.nabble.com/Rgraphviz-install- td878526.html >>> >> >> >> > >>> >> >> >> > The actual link within the above R post was: >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > http://www.graphviz.org/pub/graphviz/stable/windows/gra phviz-2.20.3.1.msi >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > The directory to Graphviz on my computer is 'c:\Program Files >>> >> >> >> > (x86)\Graphviz2.20' and the file 'libcdt-4.dll' is located in >>> >> >> >> > the >>> >> >> >> > folder >>> >> >> >> > 'c:\Program Files (x86)\Graphviz2.20\bin'. ?The following >>> >> >> >> > appears >>> >> >> >> > at >>> >> >> >> > the >>> >> >> >> > end of my path statement 'Program Files >>> >> >> >> > (x86)\Graphvis2.20\bin' >>> >> >> >> > and >>> >> >> >> > is >>> >> >> >> > also >>> >> >> >> > displayed when I type 'C:\echo %PATH%' in a command window. >>> >> >> >> > >>> >> >> >> >>> >> >> >> Can you send the full output of the echo %PATH% command? >>> >> >> >> Note that "Graphviz" is mis-spelled above. Could that be the >>> >> >> >> problem? >>> >> >> >> >>> >> >> >> >>> >> >> >> Also note that if you set your PATH in Control Panel, you need >>> >> >> >> to >>> >> >> >> start a new command window after making the change, because the >>> >> >> >> change >>> >> >> >> will not be reflected in any currently open command windows. >>> >> >> >> >>> >> >> >> > The directory to R on my computer is 'c:\Program >>> >> >> >> > Files\R\R-2.15.0\'. >>> >> >> >> > >>> >> >> >> > When I try to install 'Rgraphviz' I get the following messages >>> >> >> >> > within >>> >> >> >> > R: >>> >> >> >> > >>> >> >> >> > >>> >> >> >> >> source("http://bioconductor.org/biocLite.R") >>> >> >> >> > >>> >> >> >> > BiocInstaller version 1.4.4, ?biocLite for help >>> >> >> >> > >>> >> >> >> >> biocLite("Rgraphviz") >>> >> >> >> > >>> >> >> >> > BioC_mirror: http://bioconductor.org >>> >> >> >> > Using R version 2.15, BiocInstaller version 1.4.4. >>> >> >> >> > Installing package(s) 'Rgraphviz' >>> >> >> >> > trying URL ' >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > http://www.bioconductor.org/packages/2.10/bioc/bin/wind ows/contrib/2.15/Rgraphviz_1.34.0.zip >>> >> >> >> > ' >>> >> >> >> > Content type 'application/zip' length 936601 bytes (914 Kb) >>> >> >> >> > opened URL >>> >> >> >> > downloaded 914 Kb >>> >> >> >> > >>> >> >> >> > package ?Rgraphviz? successfully unpacked and MD5 sums checked >>> >> >> >> > >>> >> >> >> > The downloaded binary packages are in >>> >> >> >> > ? ? ? ?C:\Users\Mark W >>> >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages >>> >> >> >> > Warning message: >>> >> >> >> > installed directory not writable, cannot update packages >>> >> >> >> > 'foreign', >>> >> >> >> > 'MASS', >>> >> >> >> > ?'mgcv', 'nlme', 'survival' >>> >> >> >> > >>> >> >> >> >> >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > The file 'Rgraphviz_1.34.0.zip' is placed in 'C:\Users\Mark W >>> >> >> >> > Miller\AppData\Local\Temp\Rtmpqyh1A3\downloaded_packages' and >>> >> >> >> > the >>> >> >> >> > package >>> >> >> >> > 'Rgraphviz' does not appear in the R library in 'c:\Program >>> >> >> >> > Files\R\R-2.15.0\library'. ?Rather 'Rgraphviz' appears in >>> >> >> >> > 'C:\users\Mark >>> >> >> >> > W >>> >> >> >> > Miller\Documents\R\win-library\2.15' >>> >> >> >> > >>> >> >> >> >>> >> >> >> This is ok. >>> >> >> >> >>> >> >> >> >>> >> >> >> > I have copied and pasted the 'Rgraphviz' folder from >>> >> >> >> > 'C:\users\Mark W >>> >> >> >> > Miller\Documents\R\win-library\2.15' into 'C:\Program >>> >> >> >> > Files\R\R-2.15.0\library\'. >>> >> >> >> >>> >> >> >> >>> >> >> >> You do not need to do this. >>> >> >> >> >>> >> >> >> > >>> >> >> >> > Then inside R I type 'library('Rgraphviz')' and get the >>> >> >> >> > following >>> >> >> >> > message >>> >> >> >> > in a pop-up window: >>> >> >> >> > >>> >> >> >> > 'DP_LocalAvatar: Rgui.exe - System Error' 'The program can't >>> >> >> >> > start >>> >> >> >> > because >>> >> >> >> > libcdt-4.dll is missing from your computer. Try reinstalling >>> >> >> >> > the >>> >> >> >> > program >>> >> >> >> > to >>> >> >> >> > fix the problem.' >>> >> >> >> > >>> >> >> >> > and the following messages within R: >>> >> >> >> > >>> >> >> >> > >>> >> >> >> >> library('Rgraphviz') >>> >> >> >> > >>> >> >> >> > Loading required package: graph >>> >> >> >> > Loading required package: grid >>> >> >> >> > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', >>> >> >> >> > details: >>> >> >> >> > ?call: value[[3L]](cond) >>> >> >> >> > ?error: unable to load shared object 'C:/Users/Mark W >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > Miller/Documents/R/win- library/2.15/Rgraphviz/libs/x64/Rgraphviz.dll': >>> >> >> >> > ?LoadLibrary failure: ?The specified module could not be >>> >> >> >> > found. >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > ?Check that (1) graphviz is installed on your system; (2) the >>> >> >> >> > ?installed version of graphviz matches '2.20.3'; this is the >>> >> >> >> > version >>> >> >> >> > ?used to build this Rgraphviz package; (3) graphviz is >>> >> >> >> > accessible >>> >> >> >> > to >>> >> >> >> > ?R, e.g., the path to the graphviz 'bin' directory is in the >>> >> >> >> > system >>> >> >> >> > ?'PATH' variable. ?See additional instructions in the 'README' >>> >> >> >> > file >>> >> >> >> > of >>> >> >> >> > ?the Rgraphviz 'source' distribution, available at >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >>> >> >> >> > >>> >> >> >> > ?Ask further questions on the Bioconductor mailing list >>> >> >> >> > >>> >> >> >> > ?http://bioconductor.org/docs/mailList.html >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > Error: package/namespace load failed for ?Rgraphviz? >>> >> >> >> > >>> >> >> >> >> >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > The file 'C:\Users\Mark W >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > Miller\Documents\R\win- library\2.15\Rgraphviz\libs\x64\Rgraphviz.dll' >>> >> >> >> > does >>> >> >> >> > exist in that folder and in the folder where I copied and >>> >> >> >> > pasted >>> >> >> >> > it >>> >> >> >> > into: 'c:\Program >>> >> >> >> > Files\R\r-2.15.0\library\Rgraphviz\libs\x64\'. >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > In addition to the steps described above I have tried >>> >> >> >> > countless >>> >> >> >> > variations >>> >> >> >> > over approximately 8 hours, including uninstalling R and >>> >> >> >> > re-installing >>> >> >> >> > it. >>> >> >> >> > >>> >> >> >> > During one reboot maybe 4 hours into this process I even got >>> >> >> >> > an >>> >> >> >> > error >>> >> >> >> > message on start-up and almost everything on my desktop had >>> >> >> >> > disappeared. >>> >> >> >> > ?I >>> >> >> >> > restarted the computer again and my normal desktop was >>> >> >> >> > restored. >>> >> >> >> > ?(I >>> >> >> >> > found >>> >> >> >> > a post on the internet describing something similar when >>> >> >> >> > trying to >>> >> >> >> > install >>> >> >> >> > 'Rgraphviz' but I do not know whether my experience was >>> >> >> >> > related to >>> >> >> >> > that >>> >> >> >> > previous incident.) >>> >> >> >> > >>> >> >> >> > I am hoping someone can provide detailed step-by-step >>> >> >> >> > instructions >>> >> >> >> > on >>> >> >> >> > how >>> >> >> >> > to install the package Rgraphviz and/or identify where I am >>> >> >> >> > making >>> >> >> >> > a >>> >> >> >> > mistake based on the information I have provided. ?I have >>> >> >> >> > tried to >>> >> >> >> > include >>> >> >> >> > here as much information as I can think of. ?If I can include >>> >> >> >> > additional >>> >> >> >> > helpful information please let me know. >>> >> >> >> > >>> >> >> >> > I wonder whether the above warning message is related to why I >>> >> >> >> > cannot >>> >> >> >> > install 'Rgraphviz': 'Warning message: installed directory not >>> >> >> >> > writable, >>> >> >> >> > cannot update packages 'foreign', 'MASS', 'mgcv', 'nlme', >>> >> >> >> > 'survival''. >>> >> >> >> > >>> >> >> >> >>> >> >> >> No. That is just biocLite() telling you that those packages >>> >> >> >> couldn't >>> >> >> >> be updated because they live in a directory that you can't write >>> >> >> >> to. >>> >> >> >> If you log in as an admin user you can update those packages and >>> >> >> >> make >>> >> >> >> that message go away, or you can just ignore it. >>> >> >> >> >>> >> >> >> Dan >>> >> >> >> >>> >> >> >> >>> >> >> >> > I have not previously posted on this forum. ?Hopefully I am >>> >> >> >> > following >>> >> >> >> > protocol. >>> >> >> >> > >>> >> >> >> > Thank you for any advice. >>> >> >> >> > >>> >> >> >> > Mark W. Miller >>> >> >> >> > >>> >> >> >> > ? ? ? ?[[alternative HTML version deleted]] >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > _______________________________________________ >>> >> >> >> > Bioconductor mailing list >>> >> >> >> > Bioconductor at r-project.org >>> >> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >> >> > Search the archives: >>> >> >> >> > >>> >> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > >>> >> >> > >>> >> > >>> >> > >>> > >>> > >> >> >
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