Hi,
I have started using R (noob) and RKWard recently in ubuntu 10.04. I have installed it from synaptic without a problem and it was running fine. At that stage I decided to give Rcmdr a try too. So I installed them side by side. Both of them were working. i updated the package file recently and after that I am seeing error messages and problems.
The version of R I am using is
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i486-pc-linux-gnu (32-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.
The version of RKWard installed into my computer is:
rkward --version
Qt: 4.6.2
KDE Development Platform: 4.4.5 (KDE 4.4.5)
RKWard: 0.5.5.z+0.5.6+test2
Here is a screen shot of the error message.
Any help is appreciated.
Best,
Sourav
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
This is the development version of RKWard (daily builds). We try to keep it in a "sane" state at all times, but you should note that this version is always fresh from the lab, and has only seen very limited testing. Do you recall, when you last updated rkward before this time?
Here is a screen shot of the error message.
Could you please click on the "Details" button, and copy that text to the forum?
Regards
Thomas
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I have clicked on the details button. But it does not give any details.
Alright. Too bad.
What happens, if you simply ignore the error message? Does RKWard continue to run? Any obvious deficiencies?
Also, please locate /tmp/kde-USERNAME/ in a file manager. You will find several files called rkwardXXXXX.tmp and rkward.rbackendXXXXX.tmp (one each for every time that you started RKWard in the current session). Could you post the contents of the most recent pair of these?
Regards
Thomas
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
What happens, if you simply ignore the error message?
The interface starts. But I can't load my previously saved Rdata fles.
I have tried couple of things like importing data and stuf. Nothing happens. However, I could finally load .txt file. I, myself was curious about the error codes. Therefore I copied the "command log" of my last session to pastebin.com and attached the url here http://pastebin.com/ztN8PBnG
Any obvious deficiencies?
I must admit here that I did not muster "rkward" before. However, after loading the table I can't generate a box plot or a regular scatter plot from the rkward interface. Here is the command log:
pastebin.com/Ab0uf0pA
I could be able to process the data from Rconsole in RKward. Here is the R syntax I used.
pastebin.com/kNf9eadg
And here is the output.
By chak8870 at 2011-04-21
Also, please locate /tmp/kde-USERNAME/ in a file manager. You will find several files called rkwardXXXXX.tmp and rkward.rbackendXXXXX.tmp (one each for every time that you started RKWard in the current session). Could you post the contents of the most recent pair of these?
Here it is.
pastebin.com/JiqqnvYU
And rkward.rbackend temp file
QObject::connect: Cannot queue arguments of type 'QAbstractSocket::SocketState'
(Make sure 'QAbstractSocket::SocketState' is registered using qRegisterMetaType().)
I hope this will help understand the issue better and troubleshoot.
Thanks again for all your help.
Sourav
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Thomas,
My apology. I am not a avid forum user therefore the links were not working. Also sorry about the graphics, just wanted to paste a link.
Anyway,
I am posting the links in the chronological order again.
note that you can also post to the rkward-users mailing-list, instead (but let's keep this thread on the forum, so anybody running into the same problem will be able to find all posts).
Somehow it looks like the directory where rkward can store files is configured as "/". Go to Settings->Configure RKWard->General, and change the top-most setting to something valid (default is /home/USERNAME/.rkward/). Then restart RKWard. I think that should solve most (if not all) issues you are seeing.
I can't think of any way that recent changes in the development version could have caused the setting to be broken. Do you think it's possible that you changed this setting, yourself, accidentally? (Obviously we should have some better error-handling at this point, though).
Regards
Thomas
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Somehow it looks like the directory where rkward can store files is configured as "/". Go to Settings->Configure RKWard->General, and change the top-most setting to something valid (default is /home/USERNAME/.rkward/). Then restart RKWard. I think that should solve most (if not all) issues you are seeing.
This indeed solve most of the problem. The initial error is gone.
Do you think it's possible that you changed this setting, yourself, accidentally?
Honestly, I don't know. However, the fix that you gave me, I have never changed anything on that page. Will it be an issue if I run rkward and rcommander in the same ubuntubox?
I am not sure whether this is the right place to ask the next question. I am asking anyway though. I posted my table and my graph in the previous post. I could not be able to generate the boxplot graph from the rkward-plot-boxplot (instead I had to use the Rconsole in the rkward). There is no options to plot by a group variable (which in my case is Treatment in M). Should I do boxplot from a different package? http://img222.imageshack.us/i/boxplotnocategory.png/
This option is available in the rcommander interface. Also is there a way to save the graphs as eps image from the output (rkout.html does generate a very nice report, however the default graphics quality is low)?
Also, I was working on the scatter plot the other day and I could not be able to put a regression line through the points. Do I have to use any specific package to draw a regression line? What am I missing? http://img845.imageshack.us/i/scatterplotnoregression.png/
Thanks for sticking around and helping me out with this.
Best,
Sourav
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Will it be an issue if I run rkward and rcommander in the same ubuntubox?
No. Co-installing Rcmdr and rkward on one box has never been a problem to the best of my knowledge.
There have been problems in the past with running Rcmdr inside an RKWard session. And in fact, as I just found out, the problem came back with RKWard 0.5.5. I have just fixed this in the development version, so with the next daily build, you can even run
library(Rcmdr)
inside an RKWard session.
I could not be able to generate the boxplot graph from the rkward-plot-boxplot (instead I had to use the Rconsole in the rkward)
This part of the problem is fixed, though, isn't it? I.e. you can create some boxplots?
There is no options to plot by a group variable (which in my case is Treatment in M).
Also, I was working on the scatter plot the other day and I could not be able to put a regression line through the points.
Yes, unfortunately, some of our features are still terribly rudimentary. You will have to look into the underlying R code, or use other packages, in these cases (or, in the case of the box plot: re-organize your data). And of course help with improving our dialogs is always welcome. See http://rkward.sourceforge.net/documents/devel/plugins/index.html for information on how to do that.
Also is there a way to save the graphs as eps image from the output (rkout.html does generate a very nice report, however the default graphics quality is low)?
You can change the file format and quality used for rkout.html in Settings->Configure RKWard->Output. EPS is not a supported option, here, but SVG is. To get at EPS images (and a variety of other formates), typically the fastest way is this: In the plot dialog, check the "Preview" box. Once satisfied with the preview, in the preview window, select Device->Export… from the menu.
Regards
Thomas
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
No. Co-installing Rcmdr and rkward on one box has never been a problem to the best of my knowledge
Thanks for the info. I have installed them side by side and will use them according to the need.
you can create some boxplots?
Yes. I must admit I can create box plots. Now I am going to look into the plugins to tweak it to my need.
You can change the file format and quality used for rkout.html in Settings->Configure RKWard->Output. EPS is not a supported option, here, but SVG is. To get at EPS images (and a variety of other formates), typically the fastest way is this: In the plot dialog, check the "Preview" box. Once satisfied with the preview, in the preview window, select Device->Export… from the menu.
Thanks for this. I found it and it is very handy. SVG works as great as eps. Besides, I found the eps option according to your suggestion which solved my issue.
Yes, unfortunately, some of our features are still terribly rudimentary.
May be some of it is rudimentary but the program you gave us is customizable.
The current issues are all resolved with your help. Thanks for giving us such a powerful nice interface as well as prompt support.
Best,
Sourav
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I have started using R (noob) and RKWard recently in ubuntu 10.04. I have installed it from synaptic without a problem and it was running fine. At that stage I decided to give Rcmdr a try too. So I installed them side by side. Both of them were working. i updated the package file recently and after that I am seeing error messages and problems.
The version of R I am using is
The version of RKWard installed into my computer is:
Here is a screen shot of the error message.
Any help is appreciated.
Best,
Sourav
Hi!
This is the development version of RKWard (daily builds). We try to keep it in a "sane" state at all times, but you should note that this version is always fresh from the lab, and has only seen very limited testing. Do you recall, when you last updated rkward before this time?
Could you please click on the "Details" button, and copy that text to the forum?
Regards
Thomas
Thank you Thomas. That is a very prompt reply.
I do understand that it might be unstable to certain extent but as I said it was working absolutely fine for a week or two.
Unfortunately I don't. However, after the problem appeared I have uninstalled and reinstalled all r-cran- related packages and rkward too.
I have clicked on the details button. But it does not give any details.
Thanks.
Sourav
Alright. Too bad.
What happens, if you simply ignore the error message? Does RKWard continue to run? Any obvious deficiencies?
Also, please locate /tmp/kde-USERNAME/ in a file manager. You will find several files called rkwardXXXXX.tmp and rkward.rbackendXXXXX.tmp (one each for every time that you started RKWard in the current session). Could you post the contents of the most recent pair of these?
Regards
Thomas
Hi Thomas,
Thanks again for a quick reply.
The interface starts. But I can't load my previously saved Rdata fles.
I have tried couple of things like importing data and stuf. Nothing happens. However, I could finally load .txt file. I, myself was curious about the error codes. Therefore I copied the "command log" of my last session to pastebin.com and attached the url here
http://pastebin.com/ztN8PBnG
I must admit here that I did not muster "rkward" before. However, after loading the table I can't generate a box plot or a regular scatter plot from the rkward interface. Here is the command log:
pastebin.com/Ab0uf0pA
I could be able to process the data from Rconsole in RKward. Here is the R syntax I used.
pastebin.com/kNf9eadg
And here is the output.
By chak8870 at 2011-04-21
Here it is.
pastebin.com/JiqqnvYU
And rkward.rbackend temp file
I hope this will help understand the issue better and troubleshoot.
Thanks again for all your help.
Sourav
Hi Thomas,
My apology. I am not a avid forum user therefore the links were not working. Also sorry about the graphics, just wanted to paste a link.
Anyway,
I am posting the links in the chronological order again.
http://pastebin.com/ztN8PBnG
http://pastebin.com/Ab0uf0pA
http://pastebin.com/kNf9eadg
http://pastebin.com/JiqqnvYU
Thanks and sorry about duplicate posting.
Best,
Sourav
Hi Sourav,
note that you can also post to the rkward-users mailing-list, instead (but let's keep this thread on the forum, so anybody running into the same problem will be able to find all posts).
Somehow it looks like the directory where rkward can store files is configured as "/". Go to Settings->Configure RKWard->General, and change the top-most setting to something valid (default is /home/USERNAME/.rkward/). Then restart RKWard. I think that should solve most (if not all) issues you are seeing.
I can't think of any way that recent changes in the development version could have caused the setting to be broken. Do you think it's possible that you changed this setting, yourself, accidentally? (Obviously we should have some better error-handling at this point, though).
Regards
Thomas
Hi Thomas,
Thanks again for prompt reply.
This indeed solve most of the problem. The initial error is gone.
Honestly, I don't know. However, the fix that you gave me, I have never changed anything on that page.
Will it be an issue if I run rkward and rcommander in the same ubuntubox?
I am not sure whether this is the right place to ask the next question. I am asking anyway though. I posted my table and my graph in the previous post. I could not be able to generate the boxplot graph from the rkward-plot-boxplot (instead I had to use the Rconsole in the rkward). There is no options to plot by a group variable (which in my case is Treatment in M). Should I do boxplot from a different package?
http://img222.imageshack.us/i/boxplotnocategory.png/
This option is available in the rcommander interface. Also is there a way to save the graphs as eps image from the output (rkout.html does generate a very nice report, however the default graphics quality is low)?
Also, I was working on the scatter plot the other day and I could not be able to put a regression line through the points. Do I have to use any specific package to draw a regression line? What am I missing?
http://img845.imageshack.us/i/scatterplotnoregression.png/
Thanks for sticking around and helping me out with this.
Best,
Sourav
http://img651.imageshack.us/i/rkwardboxplotinterface.png/
I hope this image will illustrate one of the issue at least.
Thanks.
Sourav
No. Co-installing Rcmdr and rkward on one box has never been a problem to the best of my knowledge.
There have been problems in the past with running Rcmdr inside an RKWard session. And in fact, as I just found out, the problem came back with RKWard 0.5.5. I have just fixed this in the development version, so with the next daily build, you can even run
inside an RKWard session.
This part of the problem is fixed, though, isn't it? I.e. you can create some boxplots?
Yes, unfortunately, some of our features are still terribly rudimentary. You will have to look into the underlying R code, or use other packages, in these cases (or, in the case of the box plot: re-organize your data). And of course help with improving our dialogs is always welcome. See http://rkward.sourceforge.net/documents/devel/plugins/index.html for information on how to do that.
You can change the file format and quality used for rkout.html in Settings->Configure RKWard->Output. EPS is not a supported option, here, but SVG is. To get at EPS images (and a variety of other formates), typically the fastest way is this: In the plot dialog, check the "Preview" box. Once satisfied with the preview, in the preview window, select Device->Export… from the menu.
Regards
Thomas
Hi Thomas,
Once again I appreciate your prompt reply.
Thanks for the info. I have installed them side by side and will use them according to the need.
Yes. I must admit I can create box plots. Now I am going to look into the plugins to tweak it to my need.
Thanks for this. I found it and it is very handy. SVG works as great as eps. Besides, I found the eps option according to your suggestion which solved my issue.
May be some of it is rudimentary but the program you gave us is customizable.
The current issues are all resolved with your help. Thanks for giving us such a powerful nice interface as well as prompt support.
Best,
Sourav