R help - Mar 2014 - RTools and previous Cygwin installation--conflict?

Background:
?? ?--I already had the latest 64 bit cygwin (1.7.28) installed on my Windows 7
box
?? ?--I am a new R user; I just installed the latest 64 bit R today (3.0.3)
?? ?--a coworker told me that I also need to install RTools, so, I also
installed the latest RTools (3.1) from
?? ??? ?http://cran.r-project.org/bin/windows/Rtools/
?? ?--during RTools installation, I accepted all the defaults, including
"Cygwin DLLs"
?? ?--the sole additional item is that I checked to modify my PATH system env
var

~~~~~~~~~~

So what's my concern?? That modifed PATH system env var.? After
installation, PATH looks like
?? ?c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;...;<my cygwin 64 bit path>
So the RTools stuff is before my original cygwin path.

This choice means that RTools should work just fine.

***But will it screw up my normal cygwin sessions?***

In particular, if during a cygwin session a command is needed and a command with
that name is found in Rtools, I assume that that version will be used.? But it
may not be the newer one expected by cygwin--could that cause problems?

Warren Young's very detailed answer here
??
?https://stackoverflow.com/questions/18329233/is-it-advisable-to-switch-from-cygwin-32bit-to-cygwin-64bit
indicates that 32 and 64 bit cygwin do not mix well...

~~~~~~~~~~

Some more info.

I accepted the installer's default to include "Cygwin DLLs", even
tho I already had 64 bit cygwin installed, because of this note:

?? ?"The Cygwin tools have been updated to versions current as of November
19, 2013. Cygwin now builds separate 32 bit and 64 bit versions; we include 32
bit versions of the tools. If your system only has 64 bit Cygwin DLLs installed,
you will need to add our Cygwin DLLs to your path (or install the 32 bit Cygwin
DLLs into Cygwin)."
?? ?http://cran.r-project.org/bin/windows/Rtools/

But while web searching this issue, I came across a contrary recommendation:

?? ?"Some of the R tools use the Cygwin DLLs, which are included.? If you
already have Cygwin installed, you should not install these"
?? ?http://cran.r-project.org/bin/windows/Rtools/Rtools.txt

(That last instruction, by the way, goes back many years, at least to 2008:
?? ?http://www.r-bloggers.com/wp-content/uploads/2008/12/Rtools1.txt
)

So, which instruction should I follow?

~~~~~~~~~~

I apologize in advance if this issues has already been discussed before, but all
attempts today to search this email list's archives at
?? ?http://tolstoy.newcastle.edu.au/R/
always return 404 errors.

I found a 2008 discussion of this issue here
?? ?http://www.r-bloggers.com/rtools-and-cygwin-on-ms-windows/
which suggests temporarily hacking your PATH when launching RTools.

when I am on Windows, I use the msdos cmd shell and the Rtools when
I am building an R package.  It doesn't know anything about cygwin,
doesn't need to know anything about cygwin, and bypasses the need
to coordinate the two.

For everything else I use the cygwin bash.  the cygwin shell doesn't know
about the Rtools.

Rich

On Wed, Mar 12, 2014 at 12:10 AM, Brent <yhbrent at yahoo.com>
wrote:
> Background:
>     --I already had the latest 64 bit cygwin (1.7.28) installed on my
Windows 7 box
>     --I am a new R user; I just installed the latest 64 bit R today (3.0.3)
>     --a coworker told me that I also need to install RTools, so, I also
installed the latest RTools (3.1) from
>         http://cran.r-project.org/bin/windows/Rtools/
>     --during RTools installation, I accepted all the defaults, including
"Cygwin DLLs"
>     --the sole additional item is that I checked to modify my PATH system
env var
>
> ~~~~~~~~~~
>
> So what's my concern?  That modifed PATH system env var.  After
installation, PATH looks like
>     c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;...;<my cygwin 64 bit path>
> So the RTools stuff is before my original cygwin path.
>
> This choice means that RTools should work just fine.
>
> ***But will it screw up my normal cygwin sessions?***
>
> In particular, if during a cygwin session a command is needed and a command
with that name is found in Rtools, I assume that that version will be used.  But
it may not be the newer one expected by cygwin--could that cause problems?
>
> Warren Young's very detailed answer here
>    
https://stackoverflow.com/questions/18329233/is-it-advisable-to-switch-from-cygwin-32bit-to-cygwin-64bit
> indicates that 32 and 64 bit cygwin do not mix well...
>
> ~~~~~~~~~~
>
> Some more info.
>
> I accepted the installer's default to include "Cygwin DLLs",
even tho I already had 64 bit cygwin installed, because of this note:
>
>     "The Cygwin tools have been updated to versions current as of
November 19, 2013. Cygwin now builds separate 32 bit and 64 bit versions; we
include 32 bit versions of the tools. If your system only has 64 bit Cygwin DLLs
installed, you will need to add our Cygwin DLLs to your path (or install the 32
bit Cygwin DLLs into Cygwin)."
>     http://cran.r-project.org/bin/windows/Rtools/
>
> But while web searching this issue, I came across a contrary
recommendation:
>
>     "Some of the R tools use the Cygwin DLLs, which are included.  If
you already have Cygwin installed, you should not install these"
>     http://cran.r-project.org/bin/windows/Rtools/Rtools.txt
>
> (That last instruction, by the way, goes back many years, at least to 2008:
>     http://www.r-bloggers.com/wp-content/uploads/2008/12/Rtools1.txt
> )
>
> So, which instruction should I follow?
>
> ~~~~~~~~~~
>
> I apologize in advance if this issues has already been discussed before,
but all attempts today to search this email list's archives at
>     http://tolstoy.newcastle.edu.au/R/
> always return 404 errors.
>
> I found a 2008 discussion of this issue here
>     http://www.r-bloggers.com/rtools-and-cygwin-on-ms-windows/
> which suggests temporarily hacking your PATH when launching RTools.
>
> ______________________________________________
> 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.

On Wed, Mar 12, 2014 at 12:10 AM, Brent <yhbrent at yahoo.com>
wrote:
> Background:
>     --I already had the latest 64 bit cygwin (1.7.28) installed on my
Windows 7 box
>     --I am a new R user; I just installed the latest 64 bit R today (3.0.3)
>     --a coworker told me that I also need to install RTools, so, I also
installed the latest RTools (3.1) from
>         http://cran.r-project.org/bin/windows/Rtools/
>     --during RTools installation, I accepted all the defaults, including
"Cygwin DLLs"
>     --the sole additional item is that I checked to modify my PATH system
env var
>
> ~~~~~~~~~~
>
> So what's my concern?  That modifed PATH system env var.  After
installation, PATH looks like
>     c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;...;<my cygwin 64 bit path>
> So the RTools stuff is before my original cygwin path.
>
> This choice means that RTools should work just fine.
>
> ***But will it screw up my normal cygwin sessions?***
>
> In particular, if during a cygwin session a command is needed and a command
with that name is found in Rtools, I assume that that version will be used.  But
it may not be the newer one expected by cygwin--could that cause problems?
>
> Warren Young's very detailed answer here
>    
https://stackoverflow.com/questions/18329233/is-it-advisable-to-switch-from-cygwin-32bit-to-cygwin-64bit
> indicates that 32 and 64 bit cygwin do not mix well...
>
> ~~~~~~~~~~
>
> Some more info.
>
> I accepted the installer's default to include "Cygwin DLLs",
even tho I already had 64 bit cygwin installed, because of this note:
>
>     "The Cygwin tools have been updated to versions current as of
November 19, 2013. Cygwin now builds separate 32 bit and 64 bit versions; we
include 32 bit versions of the tools. If your system only has 64 bit Cygwin DLLs
installed, you will need to add our Cygwin DLLs to your path (or install the 32
bit Cygwin DLLs into Cygwin)."
>     http://cran.r-project.org/bin/windows/Rtools/
>
> But while web searching this issue, I came across a contrary
recommendation:
>
>     "Some of the R tools use the Cygwin DLLs, which are included.  If
you already have Cygwin installed, you should not install these"
>     http://cran.r-project.org/bin/windows/Rtools/Rtools.txt
>
> (That last instruction, by the way, goes back many years, at least to 2008:
>     http://www.r-bloggers.com/wp-content/uploads/2008/12/Rtools1.txt
> )
>
> So, which instruction should I follow?


I use a script that temporarily sets the paths to R and to Rtools only
when R is being used in order to avoid conflicts.   Change your path
back and grab this:

https://batchfiles.googlecode.com/svn/trunk/R.bat

or this alternative which temporarily converts the paths on the
current Windows console session only and is less automated but works
on more systems:
https://batchfiles.googlecode.com/svn/trunk/Rpathset.bat

Associated links are:

Documentation:
https://batchfiles.googlecode.com/svn/trunk/batchfiles.md

Convert documentation from markdown to PDF (optional, assumes pandoc installed):
https://batchfiles.googlecode.com/svn/trunk/make-batchfiles-pdf.bat

Home page:
https://code.google.com/p/batchfiles/

Discussion (use the sqldf discussion group for discussion):
https://groups.google.com/forum/?fromgroups#!forum/sqldf


-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

On 14-03-12 12:10 AM, Brent wrote:
> Background:
>      --I already had the latest 64 bit cygwin (1.7.28) installed on my
Windows 7 box
>      --I am a new R user; I just installed the latest 64 bit R today
(3.0.3)
>      --a coworker told me that I also need to install RTools, so, I also
installed the latest RTools (3.1) from
>          http://cran.r-project.org/bin/windows/Rtools/
>      --during RTools installation, I accepted all the defaults, including
"Cygwin DLLs"
>      --the sole additional item is that I checked to modify my PATH system
env var
>
> ~~~~~~~~~~
>
> So what's my concern?  That modifed PATH system env var.  After
installation, PATH looks like
>      c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;...;<my cygwin 64 bit
path>
> So the RTools stuff is before my original cygwin path.
>
> This choice means that RTools should work just fine.
>
> ***But will it screw up my normal cygwin sessions?***
>
> In particular, if during a cygwin session a command is needed and a command
with that name is found in Rtools, I assume that that version will be used.  But
it may not be the newer one expected by cygwin--could that cause problems?
>
> Warren Young's very detailed answer here
>     
https://stackoverflow.com/questions/18329233/is-it-advisable-to-switch-from-cygwin-32bit-to-cygwin-64bit
> indicates that 32 and 64 bit cygwin do not mix well...
My testing is done on 32 bit Cygwin.  Most of our tools are copies taken 
from the 32 bit Cygwin build, but a few of them have local 
modifications: file, make, sh and tar.  See the README.txt file for the 
discussion.  Those ones will need 32 bit Cygwin DLLs available, and the 
last time I tested several years ago, R would not build with the Cygwin 
versions of those tools.

So my advice to you would be one of the following:

1.  Just use 32 bit Cygwin all the time with Rtools first in the path, 
and things should work unless you really need the true Cygwin versions 
of those 4 tools mentioned above.

2.  Set up a separate shell to use when using the R tools.  I would 
guess the R tools would work in a 64 bit bash shell with Rtools first on 
the path, but I haven't tested.  I would not trust the advice in the 
stackoverflow article:  in particular, do not use any Cygwin version of 
R.  We do not support them and as far as I know they do not pass the 
self tests.

You can use the native 64 bit Windows build of R as long as Windows 
supports 64 bit executables; it doesn't matter whether it is launched by 
32 or 64 bit Cygwin.  So for almost everyone, (1) would be the best 
choice.  You only need 64 bit Cygwin if you are building 64 bit Cygwin 
programs and they need lots of memory.
>
> ~~~~~~~~~~
>
> Some more info.
>
> I accepted the installer's default to include "Cygwin DLLs",
even tho I already had 64 bit cygwin installed, because of this note:
>
>      "The Cygwin tools have been updated to versions current as of
November 19, 2013. Cygwin now builds separate 32 bit and 64 bit versions; we
include 32 bit versions of the tools. If your system only has 64 bit Cygwin DLLs
installed, you will need to add our Cygwin DLLs to your path (or install the 32
bit Cygwin DLLs into Cygwin)."
>      http://cran.r-project.org/bin/windows/Rtools/
>
> But while web searching this issue, I came across a contrary
recommendation:
>
>      "Some of the R tools use the Cygwin DLLs, which are included.  If
you already have Cygwin installed, you should not install these"
>      http://cran.r-project.org/bin/windows/Rtools/Rtools.txt
>
That should be updated to say "if you already have 32 bit Cygwin
installed".

Duncan Murdoch
> (That last instruction, by the way, goes back many years, at least to 2008:
>      http://www.r-bloggers.com/wp-content/uploads/2008/12/Rtools1.txt
> )
>
> So, which instruction should I follow?
>
> ~~~~~~~~~~
>
> I apologize in advance if this issues has already been discussed before,
but all attempts today to search this email list's archives at
>      http://tolstoy.newcastle.edu.au/R/
> always return 404 errors.
>
> I found a 2008 discussion of this issue here
>      http://www.r-bloggers.com/rtools-and-cygwin-on-ms-windows/
> which suggests temporarily hacking your PATH when launching RTools.
>
> ______________________________________________
> 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: so good to get a reply from the RTools maintainer! I decided for now to
go with your simplest suggestion 1.? So, I deinstalled 64 bit cygwin,
reinstalled the 32 bit version, and hope that the RTools versions of the
commands which will get picked up earlier in the PATH will not cause my cygwin
any problems.


Gabor: if I ever find Duncan's 
suggestion 1 inadequate, such as if I really need 64 bit cygwin, then I 
will adapt one of your scripts.? Your scripts, by the way, deserve 
special commendation: the code is beautiful, which is no easy feat in 
DOS...