Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
Hi Gabor: I tried the link below, but it seems to be broken. -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Friday, May 04, 2007 10:05 AM To: Doran, Harold Cc: Duncan Murdoch; r-help@stat.math.ethz.ch Subject: [SPAM] - Re: [R] R package development in windows - Bayesian Filter detected spam Regarding your comments on changing paths, 1. Rcmd.bat in the batchfiles distribution http://code.google.com/p/batchfiles/ can be used to avoid having to change the path (other than path changes required for perl and tex which you would probably want anyways to be able to use those). You will only have to place Rcmd.bat, hhc.exe and the tools somewhere in your existing path. I keep a \bin directory in my path for that purpose. It also allows you to avoid having to change paths when you install a new version of R. Also in the batchfiles distribution is Rfind.bat that will search your system and try to find the various tools on it. Its display only so it should be safe to use and can help you determine if something is missing and where various tools are on your machine. 2. Also did you follow up on my suggestions? There are TWO relevant links in the Links section of the batchfiles home page http://code.google.com/p/batchfiles/ as I mentioned in my prior emails: HowTo: Create an R Package HowTo: Create an R Package (manuals) The first gives step by step instructions and the second is a link to the authoritative source, the manuals and BOTH of them should be read, not just the manuals. On 5/4/07, Doran, Harold [EMAIL PROTECTED] wrote: OK, so I just want to go on record as noting that following the instructions exactly (exactly, exactly, exactly, emphatically) on the web given by Duncan, Gabor, and Tony at the page below, and following the instructions in Writing R Extensions results in a successful Windows build of a package. Should this email turn up in someones search using RSiteSearch() or elsewhere, my best advice is to ignore all other documents on the web attempting to explain this. I personally went through 4 or 5 different personal web sites looking for a straightforward guide. After a week or so of late night reading and experimentation, all of those documents led me to a path of failure. After reading the info on the link below, and then referring back to Writing R Extensions, I was able to build the package in only a few hours of time. It took significantly less time to read the manual and information on the link below than it did to google help pages on the topic, read those, and end up even more confused. I'm not in the best position to offer specific recommendations on how to improve this process. The reality is that after collecting all programs required, making the required changes to the path, the Rcmd commands for the build are very simple. So, the biggest task is the collection of essential programs and modification to the path. Obviously, Rtools is designed to move forward in this direction. Its current phase still doesn't automate that collection and modification process entirely, and the reasons are given on Duncan's web site. However, I suppose the only good recommendation I can make at this point is to still move forward with Rtools such that it installs all required programs and automatically updates the path accordingly. Maybe this can even become part of the base installation. Since the open source nature of R encourages development, the tools needed for development should be readily available. I am certain this recommendation is not novel, and Duncan et al have already thought of this. But, it's my attempt to do a little better than complain. The only other piece of advice I can offer is to keep this stable. That is, when R 2.5.1 et seq are released, I beg of the developers not to require a new collection of tools or a different set up than what is already required. It is a bit of work, and if changes are required at each R release, this may be too disheartening. Harold -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: Thursday, May 03, 2007 3:51 PM To: Doran, Harold Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch Subject: [SPAM] - Re: [SPAM] - Re: [R] R package development in windows - Bayesian Filter detected spam - Bayesian Filter detected spam On 5/3/2007 3:33 PM, Doran, Harold wrote: Thanks, Duncan. I'll look into that. Is there an authoritative document that codifies the new package development procedures for 2.5.0 (windows-specific), or is that Writing R Extensions? In this thread alone I've received multiple emails pointing to multiple web sites with instructions for windows. Inasmuch as its appreciated, I'm
Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
I was able to click the link in your reply and it worked so there is some problem with your email viewer. You can google for: code google batchfiles and use the first hit or type the URL in by hand. On 5/4/07, Doran, Harold [EMAIL PROTECTED] wrote: Hi Gabor: I tried the link below, but it seems to be broken. -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Friday, May 04, 2007 10:05 AM To: Doran, Harold Cc: Duncan Murdoch; r-help@stat.math.ethz.ch Subject: [SPAM] - Re: [R] R package development in windows - Bayesian Filter detected spam Regarding your comments on changing paths, 1. Rcmd.bat in the batchfiles distribution http://code.google.com/p/batchfiles/ can be used to avoid having to change the path (other than path changes required for perl and tex which you would probably want anyways to be able to use those). You will only have to place Rcmd.bat, hhc.exe and the tools somewhere in your existing path. I keep a \bin directory in my path for that purpose. It also allows you to avoid having to change paths when you install a new version of R. Also in the batchfiles distribution is Rfind.bat that will search your system and try to find the various tools on it. Its display only so it should be safe to use and can help you determine if something is missing and where various tools are on your machine. 2. Also did you follow up on my suggestions? There are TWO relevant links in the Links section of the batchfiles home page http://code.google.com/p/batchfiles/ as I mentioned in my prior emails: HowTo: Create an R Package HowTo: Create an R Package (manuals) The first gives step by step instructions and the second is a link to the authoritative source, the manuals and BOTH of them should be read, not just the manuals. On 5/4/07, Doran, Harold [EMAIL PROTECTED] wrote: OK, so I just want to go on record as noting that following the instructions exactly (exactly, exactly, exactly, emphatically) on the web given by Duncan, Gabor, and Tony at the page below, and following the instructions in Writing R Extensions results in a successful Windows build of a package. Should this email turn up in someones search using RSiteSearch() or elsewhere, my best advice is to ignore all other documents on the web attempting to explain this. I personally went through 4 or 5 different personal web sites looking for a straightforward guide. After a week or so of late night reading and experimentation, all of those documents led me to a path of failure. After reading the info on the link below, and then referring back to Writing R Extensions, I was able to build the package in only a few hours of time. It took significantly less time to read the manual and information on the link below than it did to google help pages on the topic, read those, and end up even more confused. I'm not in the best position to offer specific recommendations on how to improve this process. The reality is that after collecting all programs required, making the required changes to the path, the Rcmd commands for the build are very simple. So, the biggest task is the collection of essential programs and modification to the path. Obviously, Rtools is designed to move forward in this direction. Its current phase still doesn't automate that collection and modification process entirely, and the reasons are given on Duncan's web site. However, I suppose the only good recommendation I can make at this point is to still move forward with Rtools such that it installs all required programs and automatically updates the path accordingly. Maybe this can even become part of the base installation. Since the open source nature of R encourages development, the tools needed for development should be readily available. I am certain this recommendation is not novel, and Duncan et al have already thought of this. But, it's my attempt to do a little better than complain. The only other piece of advice I can offer is to keep this stable. That is, when R 2.5.1 et seq are released, I beg of the developers not to require a new collection of tools or a different set up than what is already required. It is a bit of work, and if changes are required at each R release, this may be too disheartening. Harold -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: Thursday, May 03, 2007 3:51 PM To: Doran, Harold Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch Subject: [SPAM] - Re: [SPAM] - Re: [R] R package development in windows - Bayesian Filter detected spam - Bayesian Filter detected spam On 5/3/2007 3:33 PM, Doran, Harold wrote: Thanks, Duncan. I'll look into that. Is there an authoritative
Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
The best, of course, would be to get rid of Perl altogether. In Python, it is possible to make standalone executables. Is it possible to also do this in Perl, then one could eliminate a perl install. Or, is it possible to use Python to accomplish what perl is currently doing? I may be getting in over my head here since I really don't know what perl is doing under the hood. Harold __ R-help@stat.math.ethz.ch 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] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
Just googling I found this: http://www.perlmonks.org/?node_id=186402 On 5/4/07, Doran, Harold [EMAIL PROTECTED] wrote: The best, of course, would be to get rid of Perl altogether. In Python, it is possible to make standalone executables. Is it possible to also do this in Perl, then one could eliminate a perl install. Or, is it possible to use Python to accomplish what perl is currently doing? I may be getting in over my head here since I really don't know what perl is doing under the hood. Harold __ R-help@stat.math.ethz.ch 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] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here that
include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html
#
Wi
n-Win
I've read through Writing R Extensions and various other
helpful web
sites. I've installed all relevant software (perl,
cygwin, mingwin,
hhc.exe). Here is what I have done so far:
1) Sourced data and functions into R
2) Used package.skeleton
3) Edited Description file
4) Edited my windows path to ensure the new programs (e.g.,
perl) are
in the path
5) Then, I open DOS and do the following in the script below
C:\Program Files\R\R-2.4.1\binRcmd build --force
--binary g:\foo
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ...'sh' is not
recognized as
an internal or external command, operable program or batch file.
OK
* removing junk files
'sh
Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
On 5/3/2007 3:33 PM, Doran, Harold wrote:
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
The manuals are the authoritative reference. Writing R Extensions tells
you what to do to set up a package. The R Administration and
Installation manual tells you how to set up your system so those
instructions will work. On Windows, you want to pay particular
attention to the appendix of the Admin manual called The Windows
Toolset. This is Appendix E in the distributed .pdf; an HTML version is
available here:
http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
We realize that these instructions are not easy to follow, there's no
need to tell us that. However, specific corrections or improvements
would be welcome.
Duncan Murdoch
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here that
include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html
#
Wi
n-Win
I've read through Writing R Extensions and various
