Re: [R] Cannot read or write to file in Linux Ubuntu
Relative paths are not a mystery nor are they solely an aspect of linux. They are in fact the norm in DOS and Windows as well as in Linux or any other file system that use a tree structure. Oh, is that all! I just never thought of that behaviour as 'relative paths' just as something that one had to take into account in DOS. I may take a look at R Studio but so far I have been comfortable with a text editor and either RGUI or a terminal. thanks John Kane Kingston ON Canada -Original Message- From: j...@surewest.net Sent: Fri, 4 May 2012 18:35:31 -0700 To: r-help@r-project.org Subject: Re: [R] Cannot read or write to file in Linux Ubuntu On Thu, 3 May 2012 10:50:46 -0800 John Kane jrkrid...@inbox.com wrote: Thanks Jeff and Sarah. I was thinking mainly of using the base path and paste routine which is something I do in Windows It will take me a while to figrue out relative paths. Relative paths are not a mystery nor are they solely an aspect of linux. They are in fact the norm in DOS and Windows as well as in Linux or any other file system that use a tree structure. Since Windows constrains you to a graphic interface, when using the file manager, you see the default use of relative paths without recognizing the behaviour. When opening or saving a file in Windows, the system will often offer you the choice of 'save, or 'save as' and if you mistakenly use 'save' from the wrong working directory, you may well have a files written other than where you thought it was. This problem is so common that Windows users tend to take it in stride and have developed habits that limit the aggravation. You do not have those habits for Linux yet. Until you are more comfortable in Linux you might want to run RStudio while using R. The learning curve of a new OS as well as different details in simply using the computer interface is quite challenging. JWDougherty __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
On Thu, 3 May 2012 10:50:46 -0800 John Kane jrkrid...@inbox.com wrote: Thanks Jeff and Sarah. I was thinking mainly of using the base path and paste routine which is something I do in Windows It will take me a while to figrue out relative paths. Relative paths are not a mystery nor are they solely an aspect of linux. They are in fact the norm in DOS and Windows as well as in Linux or any other file system that use a tree structure. Since Windows constrains you to a graphic interface, when using the file manager, you see the default use of relative paths without recognizing the behaviour. When opening or saving a file in Windows, the system will often offer you the choice of 'save, or 'save as' and if you mistakenly use 'save' from the wrong working directory, you may well have a files written other than where you thought it was. This problem is so common that Windows users tend to take it in stride and have developed habits that limit the aggravation. You do not have those habits for Linux yet. Until you are more comfortable in Linux you might want to run RStudio while using R. The learning curve of a new OS as well as different details in simply using the computer interface is quite challenging. JWDougherty __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Cannot read or write to file in Linux Ubuntu
I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base John Kane Kingston ON Canada FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
Hi John, You're probably messing up the path, just as you suspect. If you use a relative path, like you are doing, then R looks for that location starting at R's current working directory, visible with getwd(). For linux, that's the location at which you started R if you started it from a terminal. The safest solution is to use an absolute path, which will likely be something resembling /home/john/DATA/... etc - note that it will always start with a / and go from there. If you know how to start a terminal window and cd to where your file is, pwd at the command prompt will give you the absolute path to that location, which is what you should be using until you get more comfortable with the file system. The error message means that R can't find the directory you're telling it to use. Sarah On Thu, May 3, 2012 at 12:21 PM, John Kane jrkrid...@inbox.com wrote: I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
All of your tests are with relative paths. Use getwd() identify your starting directory, and if it isn't you can use setwd() to start in the right place. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. John Kane jrkrid...@inbox.com wrote: I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base John Kane Kingston ON Canada FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
Thanks. I had not realsed there were relative paths until Sarah mentioned them. It's working now: see my post to Sarah. John Kane Kingston ON Canada -Original Message- From: jdnew...@dcn.davis.ca.us Sent: Thu, 03 May 2012 09:30:10 -0700 To: jrkrid...@inbox.com, r-help@r-project.org Subject: Re: [R] Cannot read or write to file in Linux Ubuntu All of your tests are with relative paths. Use getwd() identify your starting directory, and if it isn't you can use setwd() to start in the right place. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. John Kane jrkrid...@inbox.com wrote: I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base John Kane Kingston ON Canada FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
Thanks Sarah, I suspected something like that but am still gropping around in Linux. I vaguely remember how to cd to someplace. Shades of DOS 3.2! Of was that Unixor both! Also I think I was trying to be a bit too smart-alecky in where I was placing my data folder so I moved it to my home folder to simplify figuring out the path. Still thinking in Windows terms. After a bit of trial and error: jjohn@john-K53U:~$ cd /home/john/rdata john@john-K53U:~/rdata$ dir tti.csv john@john-K53U:~/rdata$ pwd /home/john/rdata so mydata - read.csv(/home/john/rdata/tti.csv, header = TRUE) works just fine. I like the idea of staying with absolute paths. I am most appreciative. John Kane Kingston ON Canada -Original Message- From: sarah.gos...@gmail.com Sent: Thu, 3 May 2012 12:29:14 -0400 To: jrkrid...@inbox.com Subject: Re: [R] Cannot read or write to file in Linux Ubuntu Hi John, You're probably messing up the path, just as you suspect. If you use a relative path, like you are doing, then R looks for that location starting at R's current working directory, visible with getwd(). For linux, that's the location at which you started R if you started it from a terminal. The safest solution is to use an absolute path, which will likely be something resembling /home/john/DATA/... etc - note that it will always start with a / and go from there. If you know how to start a terminal window and cd to where your file is, pwd at the command prompt will give you the absolute path to that location, which is what you should be using until you get more comfortable with the file system. The error message means that R can't find the directory you're telling it to use. Sarah On Thu, May 3, 2012 at 12:21 PM, John Kane jrkrid...@inbox.com wrote: I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sarah Goslee http://www.functionaldiversity.org FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
I like the idea of staying with absolute paths. Before you write too much R code that builds in absolute paths, please consider how difficult it will be to adjust all of those paths if you need to run on a different computer or you need to reorganize your overall directory structure. If you keep related R files in the same project directory, you can collapse all of those paths down to short relative paths, and do one setwd at the beginning, or learn to manually set your base working directory as a matter of habit before each working session. (This habit is useful in more areas than just R programming.) --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. John Kane jrkrid...@inbox.com wrote: Thanks Sarah, I suspected something like that but am still gropping around in Linux. I vaguely remember how to cd to someplace. Shades of DOS 3.2! Of was that Unixor both! Also I think I was trying to be a bit too smart-alecky in where I was placing my data folder so I moved it to my home folder to simplify figuring out the path. Still thinking in Windows terms. After a bit of trial and error: jjohn@john-K53U:~$ cd /home/john/rdata john@john-K53U:~/rdata$ dir tti.csv john@john-K53U:~/rdata$ pwd /home/john/rdata so mydata - read.csv(/home/john/rdata/tti.csv, header = TRUE) works just fine. I like the idea of staying with absolute paths. I am most appreciative. John Kane Kingston ON Canada -Original Message- From: sarah.gos...@gmail.com Sent: Thu, 3 May 2012 12:29:14 -0400 To: jrkrid...@inbox.com Subject: Re: [R] Cannot read or write to file in Linux Ubuntu Hi John, You're probably messing up the path, just as you suspect. If you use a relative path, like you are doing, then R looks for that location starting at R's current working directory, visible with getwd(). For linux, that's the location at which you started R if you started it from a terminal. The safest solution is to use an absolute path, which will likely be something resembling /home/john/DATA/... etc - note that it will always start with a / and go from there. If you know how to start a terminal window and cd to where your file is, pwd at the command prompt will give you the absolute path to that location, which is what you should be using until you get more comfortable with the file system. The error message means that R can't find the directory you're telling it to use. Sarah On Thu, May 3, 2012 at 12:21 PM, John Kane jrkrid...@inbox.com wrote: I am the proud owner of a new laptop since my old one died the other day. Currently I have a dual-boot Windows 7 Home and Ubuntu 12.04 . I'll leave the Windows problems for another post. I know practically nothing about Linux so I am probably doing something stupid but ... at the moment I cannot seem read or write files in Ubuntu. I am not having any problem saving other documents to the hard drive and R , from my few simple tests, seems to be working okay otherwise. At the moment I am trying : mydata - read.csv(DATA/media/DATA/rdata/tt1.csv, header = TRUE) or mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) where tt1.csv is a text file on what, from my reading of the path listed in gedit is DATA/media/DATA/rdata The csv data is simply: aa, bb 2, 3 4, 5 What happens: --- 1 mydata - read.csv(DATA/rdata/tt1.csv, header = TRUE) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'DATA/rdata/tt1.csv': No such file or directory Am I totally screwing up the path? Or doing something else equally stupid? BTW I realise that 2.15 is out but Ubuntu as of yesterday did not have it in the repositories and I have yet to figure out how to install it from a CRAN site. 1 sessionInfo() R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sarah Goslee http://www.functionaldiversity.org
Re: [R] Cannot read or write to file in Linux Ubuntu
On Thu, May 3, 2012 at 1:53 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I like the idea of staying with absolute paths. Before you write too much R code that builds in absolute paths, please consider how difficult it will be to adjust all of those paths if you need to run on a different computer or you need to reorganize your overall directory structure. If you keep related R files in the same project directory, you can collapse all of those paths down to short relative paths, and do one setwd at the beginning, or learn to manually set your base working directory as a matter of habit before each working session. (This habit is useful in more areas than just R programming.) I agree with this, which is why I suggested you use absolute paths *until you get more comfortable with the file system.* It's a good way to diagnose your problem and figure out how to deal with paths on Linux, but not a good long-term strategy unless you expect that you will never ever move anything or change to a new computer. An intermediate solution that I use a lot is to put something like this at the beginning of R script file: basepath = /home/sarahg/whatever and then load files using something like read.table(paste(basepath, plantdata.csv, sep=/)) This eases portability between computers: I exchange a lot of analyses with postdocs, students and techs, and somehow they've not all become convinced that my way of organizing directories is the best one. Using an object with the absolute path for the data means that we can pass things back and forth with only changing one value within the script rather than all input/output commands. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cannot read or write to file in Linux Ubuntu
Thanks Jeff and Sarah. I was thinking mainly of using the base path and paste routine which is something I do in Windows It will take me a while to figrue out relative paths. John Kane Kingston ON Canada -Original Message- From: sarah.gos...@gmail.com Sent: Thu, 3 May 2012 14:07:12 -0400 To: jdnew...@dcn.davis.ca.us Subject: Re: [R] Cannot read or write to file in Linux Ubuntu On Thu, May 3, 2012 at 1:53 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I like the idea of staying with absolute paths. Before you write too much R code that builds in absolute paths, please consider how difficult it will be to adjust all of those paths if you need to run on a different computer or you need to reorganize your overall directory structure. If you keep related R files in the same project directory, you can collapse all of those paths down to short relative paths, and do one setwd at the beginning, or learn to manually set your base working directory as a matter of habit before each working session. (This habit is useful in more areas than just R programming.) I agree with this, which is why I suggested you use absolute paths *until you get more comfortable with the file system.* It's a good way to diagnose your problem and figure out how to deal with paths on Linux, but not a good long-term strategy unless you expect that you will never ever move anything or change to a new computer. An intermediate solution that I use a lot is to put something like this at the beginning of R script file: basepath = /home/sarahg/whatever and then load files using something like read.table(paste(basepath, plantdata.csv, sep=/)) This eases portability between computers: I exchange a lot of analyses with postdocs, students and techs, and somehow they've not all become convinced that my way of organizing directories is the best one. Using an object with the absolute path for the data means that we can pass things back and forth with only changing one value within the script rather than all input/output commands. Sarah -- Sarah Goslee http://www.functionaldiversity.org TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if5 Capture screenshots, upload images, edit and send them to your friends through IMs, post on Twitter®, Facebook®, MySpace™, LinkedIn® – FAST! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
