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
John Kane
Kingston ON Canada
____________________________________________________________
FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
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 <jrkrideau at 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
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 Newmiller The ..... ..... Go Live...
DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.
John Kane <jrkrideau at 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
>
>
>John Kane
>Kingston ON Canada
>
>____________________________________________________________
>FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
>
>______________________________________________
>R-help at 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.
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 at john-K53U:~$ cd /home/john/rdata
john at john-K53U:~/rdata$ dir
tti.csv
john at 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.goslee at gmail.com
> Sent: Thu, 3 May 2012 12:29:14 -0400
> To: jrkrideau at 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 <jrkrideau at 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!
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: jdnewmil at dcn.davis.ca.us > Sent: Thu, 03 May 2012 09:30:10 -0700 > To: jrkrideau at inbox.com, r-help at 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 Newmiller The ..... ..... Go > Live... > DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. > rocks...1k > --------------------------------------------------------------------------- > Sent from my phone. Please excuse my brevity. > > John Kane <jrkrideau at 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 >> >> > >John Kane > >Kingston ON Canada >> > >____________________________________________________________ > >FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! >> > >______________________________________________ > >R-help at 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!
"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: jwd at surewest.net > Sent: Fri, 4 May 2012 18:35:31 -0700 > To: r-help at 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 <jrkrideau at 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 at 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!
Hello, I have a similar issue , but in my case I am using Windows 7 i try the following command to write a dataframe to xls using the xlsReadWrite package or the write.csv function write.xls(DATA,'Reg_IDcleaned.xls') or I will write.csv replacin the suffix with .csv I get absolutely no error message and the setwd appears at top of my code with absolute path However when I look in the relevant folder ,the xls or cdv outfile is nowhere to be found. Is there a gremlin in the computer or what? Before, this write.xls was working fine and now it stopped, i used the write.csv to test if it was an error in the package. So since write.csv also fails to produce the oufile in .csv in the relevant folder, I am at my witts end -- View this message in context: http://r.789695.n4.nabble.com/Cannot-read-or-write-to-file-in-Linux-Ubuntu-tp4606457p4643025.html Sent from the R help mailing list archive at Nabble.com.