Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports >library(rgenoud) Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
Windows 7 R (32/64bit) running under cygwin: package not found
12 messages · Aldi Kraja, Jeff Newmiller, Richard M. Heiberger +3 more
On 16/10/2012 12:41 PM, Aldi Kraja wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
>library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R?
I think you'll need to debug this yourself, since you haven't given us much to work with. My guess would be that you have a different path so you're finding a different R, but it could be something else. (You aren't using the R distributed by Cygwin, are you? That one doesn't work. I don't know who put it into the Cygwin distribution, but they obviously didn't test it.) Duncan Murdoch
Thank you Duncan, No I did not install R from cygwin. R is installed with windows 7. I am calling R with a symbolic link from /usr/bin part of cygwin paths, but my symbolic link is pointing to /usr/bin/R -> /cygdrive/d/RHome/bin/R.exe Is it possible R is lost in forward paths recognized by cygwin? You are right I need to test further. Thought someone would have had this experience and a solution from previous work. Aldi
On 10/16/2012 11:51 AM, Duncan Murdoch wrote:
On 16/10/2012 12:41 PM, Aldi Kraja wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
>library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R?
I think you'll need to debug this yourself, since you haven't given us much to work with. My guess would be that you have a different path so you're finding a different R, but it could be something else. (You aren't using the R distributed by Cygwin, are you? That one doesn't work. I don't know who put it into the Cygwin distribution, but they obviously didn't test it.) Duncan Murdoch
Probably because when you run it from Cygwin the R_LIBS variable does not point to the user and install library directories. I don't know how Rgui knows where they are (registry?) but you can look in the .Library and .Library.site variables to see the results.
In a case like this, posting your sessionInfo() for each case is highly recommended.
---------------------------------------------------------------------------
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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.
Aldi Kraja <aldi at wustl.edu> wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
______________________________________________ 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.
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On 16/10/2012 1:14 PM, Aldi Kraja wrote:
Thank you Duncan, No I did not install R from cygwin. R is installed with windows 7. I am calling R with a symbolic link from /usr/bin part of cygwin paths, but my symbolic link is pointing to /usr/bin/R -> /cygdrive/d/RHome/bin/R.exe Is it possible R is lost in forward paths recognized by cygwin? You are right I need to test further. Thought someone would have had this experience and a solution from previous work.
The approach I'd use: Run rterm or rgui in the same way you were running R. Print sessionInfo() and Sys.getenv() and look for strangeness. (In the latter, look at the variables whose names start R_. See if they're different than when you successfully run R gui in the usual way.) If the interactive run works, then you could put those two diagnostics into your script, and try again. Duncan Murdoch
Aldi On 10/16/2012 11:51 AM, Duncan Murdoch wrote:
On 16/10/2012 12:41 PM, Aldi Kraja wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
>library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R?
I think you'll need to debug this yourself, since you haven't given us much to work with. My guess would be that you have a different path so you're finding a different R, but it could be something else. (You aren't using the R distributed by Cygwin, are you? That one doesn't work. I don't know who put it into the Cygwin distribution, but they obviously didn't test it.) Duncan Murdoch
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I do not think that this has anything to do with the issue at hand, but just to clarify ... On Tue, Oct 16, 2012 at 10:18 AM, Jeff Newmiller
<jdnewmil at dcn.davis.ca.us> wrote:
Probably because when you run it from Cygwin the R_LIBS variable does not point to the user and install library directories. I don't know how Rgui knows where they are (registry?)
R for Windows need not use the registry at all, and does so optionally for just a couple of minor issues. See the R for WIndows FAQ 2.17 for details. ?library ?.libPaths describe how R sets/gets library paths (including defaults). Cheers, Bert
but you can look in the .Library and .Library.site variables to see the results.
In a case like this, posting your sessionInfo() for each case is highly recommended.
---------------------------------------------------------------------------
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.
Aldi Kraja <aldi at wustl.edu> wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
______________________________________________ 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.
______________________________________________ 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.
Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
Thank you all including Bert,
In my opinion the library() when is working in cygwin env., does not
check the additional libraries, where R installed the additional packages.
So the solution for this problem was to define manually in my programs
where is located the library of additional packages:
(although I was expecting library() itself to know about the additional
packages
library('rgenoud',lib.loc='C:/Users/aldi/Documents/R/win-library/2.15')
This solved the problem. Now R works again in cygwin. :-)
Thanks,
Aldi
On 10/16/2012 1:19 PM, Bert Gunter wrote:
I do not think that this has anything to do with the issue at hand, but just to clarify ... On Tue, Oct 16, 2012 at 10:18 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
Probably because when you run it from Cygwin the R_LIBS variable does not point to the user and install library directories. I don't know how Rgui knows where they are (registry?)
R for Windows need not use the registry at all, and does so optionally for just a couple of minor issues. See the R for WIndows FAQ 2.17 for details. ?library ?.libPaths describe how R sets/gets library paths (including defaults). Cheers, Bert
but you can look in the .Library and .Library.site variables to see the results.
In a case like this, posting your sessionInfo() for each case is highly recommended.
---------------------------------------------------------------------------
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.
Aldi Kraja <aldi at wustl.edu> wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
On 16/10/2012 3:02 PM, Aldi Kraja wrote:
Thank you all including Bert,
In my opinion the library() when is working in cygwin env., does not
check the additional libraries, where R installed the additional packages.
So the solution for this problem was to define manually in my programs
where is located the library of additional packages:
(although I was expecting library() itself to know about the additional
packages
library('rgenoud',lib.loc='C:/Users/aldi/Documents/R/win-library/2.15')
This solved the problem. Now R works again in cygwin. :-)
Windows defines various environment variables to set a user's home directory, and Cygwin sets different ones. R assumes the user library is in there. I forget which variable to look in, but for you, Windows thinks your home directory is C:/Users/aldi, and Cygwin probably thinks it is something like C:/cygwin/home/aldi. You can override this by setting the R_LIBS_USER variable in Cygwin to C:/Users/aldi/Documents/R/win-library/2.15 before you start R; then things should be fine. Duncan Murdoch
Thanks, Aldi On 10/16/2012 1:19 PM, Bert Gunter wrote:
I do not think that this has anything to do with the issue at hand, but just to clarify ... On Tue, Oct 16, 2012 at 10:18 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
Probably because when you run it from Cygwin the R_LIBS variable does not point to the user and install library directories. I don't know how Rgui knows where they are (registry?)
R for Windows need not use the registry at all, and does so optionally for just a couple of minor issues. See the R for WIndows FAQ 2.17 for details. ?library ?.libPaths describe how R sets/gets library paths (including defaults). Cheers, Bert
but you can look in the .Library and .Library.site variables to see the results.
In a case like this, posting your sessionInfo() for each case is highly recommended.
---------------------------------------------------------------------------
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.
Aldi Kraja <aldi at wustl.edu> wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
______________________________________________ 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.
Duncan wrote
> You can override this by setting the R_LIBS_USER variable in Cygwin to
> C:/Users/aldi/Documents/R/win-library/2.15 before you start R; then
> things should be fine.
If you use R_LIBS_USER then you have to be careful when later calling .libPaths
to add more libraries:
% env R_LIBS_USER=/homes/bill/packages/Rlib R --quiet
> .libPaths()
[1] "/homes/bill/packages/Rlib"
[2] "/opt/sw/R/R-2.15.1.atlas1/lib/R/library"
> print(.libPaths("/tmp")) # loses library specified by R_LIBS_USER
[1] "/tmp"
[2] "/opt/sw/R/R-2.15.1.atlas1/lib/R/library"
If you use R_LIBS_SITE instead of R_LIBS_USER then your chosen library
sticks around (it is saved in base::.Library.site, which is used by .libPaths())
% env R_LIBS_SITE=/homes/bill/packages/Rlib R --quiet
> .libPaths()
[1] "/homes/bill/packages/Rlib"
[2] "/opt/sw/R/R-2.15.1.atlas1/lib/R/library"
> print(.libPaths("/tmp")) # keeps library specified by R_LIBS_SITE
[1] "/tmp"
[2] "/homes/bill/packages/Rlib"
[3] "/opt/sw/R/R-2.15.1.atlas1/lib/R/library"
The difference between R_LIBS_USER and R_LIBS_SITE seems odd to me.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Duncan Murdoch Sent: Tuesday, October 16, 2012 12:39 PM To: Aldi Kraja Cc: r-help at r-project.org; Bert Gunter Subject: Re: [R] Windows 7 R (32/64bit) running under cygwin: package not found On 16/10/2012 3:02 PM, Aldi Kraja wrote:
Thank you all including Bert,
In my opinion the library() when is working in cygwin env., does not
check the additional libraries, where R installed the additional packages.
So the solution for this problem was to define manually in my programs
where is located the library of additional packages:
(although I was expecting library() itself to know about the additional
packages
library('rgenoud',lib.loc='C:/Users/aldi/Documents/R/win-library/2.15')
This solved the problem. Now R works again in cygwin. :-)
Windows defines various environment variables to set a user's home directory, and Cygwin sets different ones. R assumes the user library is in there. I forget which variable to look in, but for you, Windows thinks your home directory is C:/Users/aldi, and Cygwin probably thinks it is something like C:/cygwin/home/aldi. You can override this by setting the R_LIBS_USER variable in Cygwin to C:/Users/aldi/Documents/R/win-library/2.15 before you start R; then things should be fine. Duncan Murdoch
Thanks, Aldi On 10/16/2012 1:19 PM, Bert Gunter wrote:
I do not think that this has anything to do with the issue at hand, but just to clarify ... On Tue, Oct 16, 2012 at 10:18 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
Probably because when you run it from Cygwin the R_LIBS variable does not point to
the user and install library directories. I don't know how Rgui knows where they are (registry?)
R for Windows need not use the registry at all, and does so optionally for just a couple of minor issues. See the R for WIndows FAQ 2.17 for details. ?library ?.libPaths describe how R sets/gets library paths (including defaults). Cheers, Bert
but you can look in the .Library and .Library.site variables to see the results.
In a case like this, posting your sessionInfo() for each case is highly recommended.
---------------------------------------------------------------------------
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.
Aldi Kraja <aldi at wustl.edu> wrote:
Hi, Using R 2.15.1 on Windows 7. Have installed both versions 32 and 64bit. In both of them among others I have installed a package rgenoud When I open R gui of 32bit and write library(rgenoud) it responds by showing a functional rgenoud version 5.7-8. The same it does on Rgui 64bit. Now I am working in cygwin (v. 1.12.4.0) with xwin. Normally before when I had installed a package, I only had to call the library with the name of the package and R will find the right one to load. Now when I apply R CMD BATCH script1.R out1.txt, under cygwin the first thing it reports: R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" After some generalities it reports
library(rgenoud)
Error in library(rgenoud) : there is no package called 'rgenoud' Execution halted So my question is why under cygwin in a batch mode, it does not find the installed package, which is already installed in my laptop's R? Thank you in advance, Aldi
______________________________________________ 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.
______________________________________________ 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.