Re: [Rd] cygwin tar?
On Wed, 17 Mar 2004 15:49:41 -0700, you wrote:
>To build R from source in a Windows system, do you 'make' from cygwin bash,
>or from a Windows command line prompt?
I currently use Cygwin's bash, but I used to use Win98's command line
prompt. I think they both still work, but the command line prompt is
not being tested much these days.
> After reading
>src/gnuwin32/{INSTALL,readme,readme.packages} and the rw-FAQ, I strongly
>suspect the shell commands in there are are intended to be run from only
>the Windows command line prompt. I couldn't find any explicit mention of
>which shell to use, but in rw-FAQ and readme.packages, the 'cd' commands
>(at least those intended for execution on Windows systems) all use backward
>slashes, which implies Windows command line. In src/gnuwin32/INSTALL, the
>'cd' commands have forward slashes, which only works with a unix-style
>shell, like bash. However I suspect those are typos.
I wouldn't pay too much attention to the direction of the slashes.
The documentation is generally written for the users who use the
standard Windows shell, so backslashes are appropriate, but the
developers mainly use Unix-like shells, so forward slashes are what we
use. In fact, forward slashes work in many places in Windows
(including the Win XP command line prompt).
Duncan Murdoch
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Re: [Rd] unit testing framework for R?
"Paul Gilbert" <[EMAIL PROTECTED]> writes:
> I am interested in this, but there is already a fair amount that can
> be accomplished within the existing framework. I do something I think
> of as unit testing, but my code chunks are packages rather than
> functions. This does not have to be reactive. With a proper makefile
> setup it can be proactive.
Correct -- it's the interface.
> Within a package it should be possible to reflect some of the
> dependancy structure simply by a naming convention like tests/01test,
> tests/02othertest, tests/03moretests
That would be the next step -- what we actually do is have functions
in the tests/ directory, along with a possible external flag variable
which if bound, disables the automatic evaluation of the functions and
instead lets one pick a suite of functions.
So our hacks are basically:
1. use a possibly bound variable to determine if we evaluate
everything (CMD check) or just pieces (test(c(1,2,10))
2. create an instance of a class that describes this.
3. have methods for the class that automate the evaluation.
> I am not sure how much will be gained by automatically generating
> comparison files for the tests. Most of my tests are based on
> computing numeric values, doing a comparison with known values, and
> executing stop()if there is a problem. If you could generate those
> kind of comparisons automatically, then that would be terrific.
I'm not constructing comparison files for the tests -- I'm
testing results against previous stored results and returning a
boolean value indicating if there is a pass.
And its a hack since we don't do it automagically (or rather,
automagically via a "sample" observation of the function's parse
tree).
One of these days I'll clean it up, but I suspect that someone will
implement it right before I get around to it (post Bioconductor
release).
best,
-tony
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RE: [Rd] unit testing framework for R?
Tony
I am interested in this, but there is already a fair amount that can be accomplished
within the existing framework. I do something I think of as unit testing, but my code
chunks are packages rather than functions. This does not have to be reactive. With a
proper makefile setup it can be proactive.
Within a package it should be possible to reflect some of the dependancy structure
simply by a naming convention like tests/01test, tests/02othertest, tests/03moretests
I am not sure how much will be gained by automatically generating comparison files for
the tests. Most of my tests are based on computing numeric values, doing a comparison
with known values, and executing stop()if there is a problem. If you could generate
those kind of comparisons automatically, then that would be terrific.
Paul Gilbert
-Original Message-
From: A.J. Rossini [mailto:[EMAIL PROTECTED]
Sent: Wed 3/17/2004 4:21 PM
To: Tony Plate
Cc: [EMAIL PROTECTED]
Subject:Re: [Rd] unit testing framework for R?
Tony Plate <[EMAIL PROTECTED]> writes:
> How would a "unit testing" framework look different? (other than
> maybe the ability to pick and choose tests easily and run them
> quickly).
That is precisely it -- i.e. it's all testing, but it depends on
where and how the tests are intended.
(and then, how easy it is to write tests and run them..).
The basic principle for unit tests is that you can associate a test
with a particular unit of code, and relate the ability to run it to
the function.
So, one approach is to use the tests directory, with a file for
each function with tests, and then have a means to test. This is
reasonably easy to do.
The other issue is the ability to group tests by dependencies (again,
more of a UI functionality than a real problem).
So, I think the point I'm trying to hammer at is the interface, not
whether a framework which can be adopted is already in place.
best,
-tony
--
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Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
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Re: [Rd] cygwin tar?
At Wednesday 05:39 AM 3/17/2004, Prof Brian Ripley wrote:
On Wed, 17 Mar 2004, Martyn Plummer wrote:
> I had the same problem as Tony with multiple copies of cygwin1.dll. But
> doesn't this solution (renaming cygwin1.dll in the tools directory) just
> link the tools with the cygwin1.dll that comes with cygwin? In which
> case will it work if the tools are linked against a different version of
> the cygwin1 library?
It may or it may not. At least some cygwin1.dll's are broken and cause
tar to malfunction.
I don't uninstall cygwin, but I do ensure that its path is not mounted,
since if it thinks there is a /bin/cygwin1.dll or /usr/bin/cygwin1.dll it
complains, even if that is really C:/packages/usr/bin/cygwin1.dll and not
in your path.
To build R from source in a Windows system, do you 'make' from cygwin bash,
or from a Windows command line prompt? After reading
src/gnuwin32/{INSTALL,readme,readme.packages} and the rw-FAQ, I strongly
suspect the shell commands in there are are intended to be run from only
the Windows command line prompt. I couldn't find any explicit mention of
which shell to use, but in rw-FAQ and readme.packages, the 'cd' commands
(at least those intended for execution on Windows systems) all use backward
slashes, which implies Windows command line. In src/gnuwin32/INSTALL, the
'cd' commands have forward slashes, which only works with a unix-style
shell, like bash. However I suspect those are typos.
Also, what did you mean by "ensure that its path is not mounted"? I tried
'umount'ing the various /bin etc directories, but still got the cygwin1.dll
conflict error when trying to run .exe's from R/tools from the cygwin bash
prompt (with no cygwin system directories on my path).
# in cygwin, after doing 'umount' on all the cygwin system directories
$ c:/cygwin/bin/mount
C:\cygwin\usr\X11R6\lib\X11\fonts on /usr/X11R6/lib/X11/fonts type system
(binmo
de)
c: on /cygdrive/c type user (textmode,noumount)
e: on /cygdrive/e type user (textmode,noumount)
f: on /cygdrive/f type user (textmode,noumount)
h: on /cygdrive/h type user (textmode,noumount)
$ type -a cygwin1.dll
cygwin1.dll is /cygdrive/c/R/tools/cygwin1.dll
$ echo $PATH
.:/cygdrive/c/R/tools:/cygdrive/c/MinGW/bin:/cygdrive/c/texmf/miktex/bin:/cygdri
ve/c/Perl/bin/cygdrive/c/Program Files/Html Help
Workshop:/cygdrive/c/gstools/gs
/gs7.03/bin:/cygdrive/c/R/rw1080/bin
$ ls
c:\R\tools\ls.exe: *** proc version mismatch detected - 0x1E4C5751/0x8E0899FA.
You have multiple copies of cygwin1.dll on your system.
Search for cygwin1.dll using the Windows Start->Find/Search facility
and delete all but the most recent version. The most recent version *should*
reside in x:\cygwin\bin, where 'x' is the drive on which you have
installed the cygwin distribution.
(All this is using a pretty up-to-date cygwin (downloaded in the last month
or so) under Windows 2000).
-- Tony Plate
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[Rd] Bundles and 1.9.0 (alpha)
What is it "Package bundles" and 1.9.0 (alpha) ?
'Rcmd check Bundle' aborts with:
Error: cannot open file '.../Bundle.Rcheck/Package/R/Package' for reading
In ".../Bundle.Rcheck/" the packages of the bundle are "merged" into a single
"package". ('Rcmd INSTALL' does also "merge" the packages of the bundle.)
I do not in "Writing R Extensions", version 1.9.0, section 1.1.5, see any
changes (relative 1.8.1) on how bundles should be handled.
I get the same on abort on the "VR" (7.1-14) bundle.
Jens Henrik Badsberg
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Re: [Rd] unit testing framework for R?
Tony Plate <[EMAIL PROTECTED]> writes:
> How would a "unit testing" framework look different? (other than
> maybe the ability to pick and choose tests easily and run them
> quickly).
That is precisely it -- i.e. it's all testing, but it depends on
where and how the tests are intended.
(and then, how easy it is to write tests and run them..).
The basic principle for unit tests is that you can associate a test
with a particular unit of code, and relate the ability to run it to
the function.
So, one approach is to use the tests directory, with a file for
each function with tests, and then have a means to test. This is
reasonably easy to do.
The other issue is the ability to group tests by dependencies (again,
more of a UI functionality than a real problem).
So, I think the point I'm trying to hammer at is the interface, not
whether a framework which can be adopted is already in place.
best,
-tony
--
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Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
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Re: [Rd] unit testing framework for R?
How would a "unit testing" framework look different? (other than maybe the ability to pick and choose tests easily and run them quickly). -- Tony Plate At Wednesday 01:01 PM 3/17/2004, A.J. Rossini wrote: the package 'tests' directory is great, and we use it, but it isn't unit testing in the same sense -- more regression tests (reactive rather than proactive). best, -tony Tony Plate <[EMAIL PROTECTED]> writes: > Packages can have a 'tests' directory, which can contain foo.R and > foo.Rout.save files. When packages are built (or checked) the output > from running R with the commands in foo.R is compared with > foo.Rout.save, and differences are reported. > > The "Writing R Extensions" manual discusses this a little. It > suggests: "Use R CMD check --help (Rcmd check --help on Windows) to > obtain more information about the usage of the R package checker. A > subset of the checking steps can be selected by adding flags." > > I've considered looking at several enhancements of the testing > features: (1) automatically construct foo.R from foo.Rout.save (easy > if the file only contains simple commands issued at the standard > prompt); (2) allow specification of which test files to run; and (3) > print summaries of test successes and failures at the end of running > the selected tests. Is there any wider interest in such features? > > -- Tony Plate > > At Wednesday 11:11 AM 3/17/2004, Paul Shannon wrote: >>In a quick search of the R website just now, I found no mention of >>a unit testing framework for R. I hope to find something >>in the style of Java's JUnit, or Python's unittest. Is such a >>thing available? >> >>Thanks, >> >> - Paul Shannon >> Institute for Systems Biology >> Seattle >> >>__ >>[EMAIL PROTECTED] mailing list >>https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > -- [EMAIL PROTECTED]http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be confidential and privileged. If you received this message in error, please destroy it and notify the sender. Thank you. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unit testing framework for R?
the package 'tests' directory is great, and we use it, but it isn't
unit testing in the same sense -- more regression tests (reactive
rather than proactive).
best,
-tony
Tony Plate <[EMAIL PROTECTED]> writes:
> Packages can have a 'tests' directory, which can contain foo.R and
> foo.Rout.save files. When packages are built (or checked) the output
> from running R with the commands in foo.R is compared with
> foo.Rout.save, and differences are reported.
>
> The "Writing R Extensions" manual discusses this a little. It
> suggests: "Use R CMD check --help (Rcmd check --help on Windows) to
> obtain more information about the usage of the R package checker. A
> subset of the checking steps can be selected by adding flags."
>
> I've considered looking at several enhancements of the testing
> features: (1) automatically construct foo.R from foo.Rout.save (easy
> if the file only contains simple commands issued at the standard
> prompt); (2) allow specification of which test files to run; and (3)
> print summaries of test successes and failures at the end of running
> the selected tests. Is there any wider interest in such features?
>
> -- Tony Plate
>
> At Wednesday 11:11 AM 3/17/2004, Paul Shannon wrote:
>>In a quick search of the R website just now, I found no mention of
>>a unit testing framework for R. I hope to find something
>>in the style of Java's JUnit, or Python's unittest. Is such a
>>thing available?
>>
>>Thanks,
>>
>> - Paul Shannon
>> Institute for Systems Biology
>> Seattle
>>
>>__
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>>https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>
> __
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> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] unit testing framework for R?
Paul Shannon <[EMAIL PROTECTED]> writes:
> In a quick search of the R website just now, I found no mention of
> a unit testing framework for R. I hope to find something
> in the style of Java's JUnit, or Python's unittest. Is such a
> thing available?
Paul -
I've got a first pass at such a thing, but it isn't clear what the
right "general purpose" solution is (currently, it consists of
a set of S4 classes which allow for comparison of results for
functions -- could be easily extended for S4 methods and classes, but
havn't had time to think it through.
best,
-tony
--
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Re: [Rd] unit testing framework for R?
Packages can have a 'tests' directory, which can contain foo.R and foo.Rout.save files. When packages are built (or checked) the output from running R with the commands in foo.R is compared with foo.Rout.save, and differences are reported. The "Writing R Extensions" manual discusses this a little. It suggests: "Use R CMD check --help (Rcmd check --help on Windows) to obtain more information about the usage of the R package checker. A subset of the checking steps can be selected by adding flags." I've considered looking at several enhancements of the testing features: (1) automatically construct foo.R from foo.Rout.save (easy if the file only contains simple commands issued at the standard prompt); (2) allow specification of which test files to run; and (3) print summaries of test successes and failures at the end of running the selected tests. Is there any wider interest in such features? -- Tony Plate At Wednesday 11:11 AM 3/17/2004, Paul Shannon wrote: In a quick search of the R website just now, I found no mention of a unit testing framework for R. I hope to find something in the style of Java's JUnit, or Python's unittest. Is such a thing available? Thanks, - Paul Shannon Institute for Systems Biology Seattle __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] unit testing framework for R?
In a quick search of the R website just now, I found no mention of a unit testing framework for R. I hope to find something in the style of Java's JUnit, or Python's unittest. Is such a thing available? Thanks, - Paul Shannon Institute for Systems Biology Seattle __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Cygwin, MSys and Rtools can be happy together (Was: RE: [Rd] cygwin tar?)
Regarding the troubles reported by others with Cygwin and MSys, I would like to point out to have both installed merrily such that you can - use Cygwin for all 'normal' work inside of rxvt/xterm. - use MSys/MingW for one main purpose: building R packages. For this to work, I use appropriate settings in the /home/$USER/.profile for MSys to set its path (with the required Tools by BDR) and then change directories into the /home/$USER for Cygwin. That gives transparent access to all files, sources, ... and yet as the Cygwin.bat will not have been executed, that session is free (enough) of the Cygwin dll to build the R packages. I could detail this further if it helps. Regards, Dirk -- The relationship between the computed price and reality is as yet unknown. -- From the pac(8) manual page __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Misspelled summary of "mle" class object (PR#6674)
But not in 1.9.0 alpha which is out for testing. I have already corrected it. On Wed, 17 Mar 2004 [EMAIL PROTECTED] wrote: > Full_Name: Vincent Goulet > Version: 1.8.1 > OS: Linux > Submission from: (NULL) (24.203.194.201) > > > In the summary of an object of class "mle", the word "Coefficients" misses an > "f": > > > ( m <- mle(f, lower=c(0,0), method="L-BFGS-B") ) This is not repoducible, BTW. > Call: > mle(minuslogl = f, method = "L-BFGS-B", lower = c(0, 0)) > > Coefficients: >alpha lambda > 2.276008 5.020003 > > summary(m) > Maximum likelihod estimation > > Call: > mle(minuslogl = f, method = "L-BFGS-B", lower = c(0, 0)) > > Coeficients: <--- !!! >Estimate Std. Error > alpha 2.276008 0.3012757 > lambda 5.020003 0.7431560 > > -2 log L: 10.71757 > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Misspelled summary of "mle" class object (PR#6674)
> "vincent" == vincent goulet <[EMAIL PROTECTED]> > on Wed, 17 Mar 2004 17:26:39 +0100 (CET) writes: vincent> Full_Name: Vincent Goulet vincent> Version: 1.8.1 vincent> OS: Linux vincent> Submission from: (NULL) (24.203.194.201) vincent> In the summary of an object of class "mle", the vincent> word "Coefficients" misses an "f": Thank you, Vincent, for the report. Note that this has been fixed months ago, and in time ranges like today where alpha versions of R are available, we would be glad if you first checked "R x.y.z. alpha" Regards, Martin Maechler, Seminar fuer Statistik, ETH Zurich SWITZERLAND __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] Misspelled summary of "mle" class object (PR#6674)
Full_Name: Vincent Goulet Version: 1.8.1 OS: Linux Submission from: (NULL) (24.203.194.201) In the summary of an object of class "mle", the word "Coefficients" misses an "f": > ( m <- mle(f, lower=c(0,0), method="L-BFGS-B") ) Call: mle(minuslogl = f, method = "L-BFGS-B", lower = c(0, 0)) Coefficients: alpha lambda 2.276008 5.020003 > summary(m) Maximum likelihod estimation Call: mle(minuslogl = f, method = "L-BFGS-B", lower = c(0, 0)) Coeficients: <--- !!! Estimate Std. Error alpha 2.276008 0.3012757 lambda 5.020003 0.7431560 -2 log L: 10.71757 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
[Rd] EBSCO Gateway: Email Content violation
Your message contained an attachment that was infected with a virus or was blocked due to file type restrictions. From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: hello Matching Subject: hello __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
Cygwin and Rtools (Was: RE: [Rd] cygwin tar?)
If it helps anyone, below is the startup script I use in WinXP to get
an MSDOS prompt that give me access to R and Ripley's Rtools so that I
can run RCMD build etc without problems and at the same time keep my
Cygwin installation. This is pretty much what Ripley suggest. Note the
"NOTE: ..." below!
I'm sorry if mine or your email client cuts the lines.
Henrik Bengtsson
-
Begin: RCMDprompt.bat
-
@echo off
rem
##
rem # Usage: RCMDprompt.bat [path]
rem #
rem # This script opens a MS-DOS prompt with a enviroment variables
rem # set such that R can be ran and packages can be build.
rem # If 'path' is given, the working directory will be set
accordingly.
rem #
rem # NOTE: This scripts works even if Cygwin is installed. HOWEVER,
you
rem # can not have any Cygwin applications running (not even a shell
or
rem # XEmacs for Cygwin) at the same time you try to run RCMD.
rem #
rem # Requires:
rem # To build and install packages two things must be installed, i.e.
rem # exists in the PATH. First, the Rtools compilation [1] by B.
Ripley
rem # must exists. The path (R_TOOLS) to it is set below. Second, Perl
rem # (must not be Cygwin/Perl) must also exists. The path to it is
set
rem # below.
rem #
rem # Reference:
rem # [1] http://www.stats.ox.ac.uk/pub/Rtools/
rem #
rem # Henrik Bengtsson, [EMAIL PROTECTED], March 2004.
rem
##
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # 1. "Global" environment variables
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # Short version of PROGRAMFILES, e.g. 'C:\Progra~1' instead of
rem # 'C:\Program Files\', which contains spaces that are BAD for R &
Co.
set PROGRAMFILES_SHORT=C:\Progra~1
rem # Directory where user directories are
set USERSDIR=C:\users
rem # Set the main R directory
set R_ROOT=%PROGRAMFILES_SHORT%\R
rem # Set the R_HOME directory
set R_HOME=%R_ROOT%\rw1081
rem set R_HOME=%R_ROOT%\rw1090alpha
rem # Set the HOME directory. This is the directory where R looks
rem # for the .Rprofile and .Renviron files. See ?Startup.
set HOME=%USERSDIR%\%USERNAME%\
rem # Set TMPDIR to a temporary directory
set TMPDIR=%TEMP%
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # 2. Setup the PATH
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # Clear the PATH (making the main Cygwin installation "invisible")
path ;
rem # Set the LaTeX directory
rem # http://www.miktex.org/
path %PROGRAMFILES%\MikTeX\miktex\bin;%PATH%
rem # Set the Microsoft HTML Help Compiler directory
rem #
http://msdn.microsoft.com/library/tools/htmlhelp/chm/HH1Start.htm
path %PROGRAMFILES%\HTML Help Workshop;%PATH%
rem # Set the Perl directory
rem # http://www.activestate.com/Products/ActivePerl/Download.html
path C:\Perl\bin;%PATH%
rem # Set the Rtools [1] directory
rem # http://www.stats.ox.ac.uk/pub/Rtools/
path %R_ROOT%\Rtools;%PATH%
rem # Set the R_HOME directory
path %R_HOME%\bin;%PATH%
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # 3. Start the MSDOS prompt in the given directory
rem # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
rem # Change directory according to argument 1
cd %1%
rem # Start the MSDOS commando prompt
%SystemRoot%\system32\cmd.exe
-
End: RCMDprompt.bat
-
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Prof
> Brian Ripley
> Sent: den 17 mars 2004 13:40
> To: Martyn Plummer
> Cc: Tony Plate; Jeff D. Hamann; [EMAIL PROTECTED]
> Subject: Re: [Rd] cygwin tar?
>
>
> On Wed, 17 Mar 2004, Martyn Plummer wrote:
>
> > I had the same problem as Tony with multiple copies of
cygwin1.dll.
> > But doesn't this solution (renaming cygwin1.dll in the tools
> > directory) just link the tools with the cygwin1.dll that comes
with
> > cygwin? In which case will it work if the tools are linked
> against a
> > different version of the cygwin1 library?
>
> It may or it may not. At least some cygwin1.dll's are broken
> and cause
> tar to malfunction.
>
> I don't uninstall cygwin, but I do ensure that its path is
> not mounted,
> since if it thinks there is a /bin/cygwin1.dll or
> /usr/bin/cygwin1.dll it
> complains, even if that is really
> C:/packages/usr/bin/cygwin1.dll and not
> in your path.
>
> > To answer Jeff's question
> > >
> > > if($WINDOWS) {
> > > ## workaround for paths in Cygwin tar
> > > $filepath =~ s+^([A-Za-x]):+/cygdrive/\1+;
> > > }
> > >
> > > in the build script and don't think it needs to be there
> since you
> > > can use the tar utility th
Re: [Rd] cygwin tar?
On Wed, 17 Mar 2004, Martyn Plummer wrote:
> I had the same problem as Tony with multiple copies of cygwin1.dll. But
> doesn't this solution (renaming cygwin1.dll in the tools directory) just
> link the tools with the cygwin1.dll that comes with cygwin? In which
> case will it work if the tools are linked against a different version of
> the cygwin1 library?
It may or it may not. At least some cygwin1.dll's are broken and cause
tar to malfunction.
I don't uninstall cygwin, but I do ensure that its path is not mounted,
since if it thinks there is a /bin/cygwin1.dll or /usr/bin/cygwin1.dll it
complains, even if that is really C:/packages/usr/bin/cygwin1.dll and not
in your path.
> To answer Jeff's question
> >
> > if($WINDOWS) {
> > ## workaround for paths in Cygwin tar
> > $filepath =~ s+^([A-Za-x]):+/cygdrive/\1+;
> > }
> >
> > in the build script and don't think it needs to be there since you can
> > use the tar utility that comes with mingw, yes?
>
> You're talking about the tar that comes with MSYS. And no you can't use
> it because it can't handle symbolic links, a problem that is discussed
> in the documentation.
That's not the only problem I have met with MSYS's tar, if that is what
was meant. It often had problems for me in the middle of .tar.gz archives
that other systems are happy with.
I do know how to solve this, but I am not going to put the effort in to do
so. So the situation will remain
`follow the instructions or don't ask for help'.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] cygwin tar?
I had the same problem as Tony with multiple copies of cygwin1.dll. But
doesn't this solution (renaming cygwin1.dll in the tools directory) just
link the tools with the cygwin1.dll that comes with cygwin? In which
case will it work if the tools are linked against a different version of
the cygwin1 library?
To answer Jeff's question
>
> if($WINDOWS) {
> ## workaround for paths in Cygwin tar
> $filepath =~ s+^([A-Za-x]):+/cygdrive/\1+;
> }
>
> in the build script and don't think it needs to be there since you can
> use the tar utility that comes with mingw, yes?
You're talking about the tar that comes with MSYS. And no you can't use
it because it can't handle symbolic links, a problem that is discussed
in the documentation.
On Tue, 2004-03-16 at 20:23, Tony Plate wrote:
> Jeff: alternatively, I don't think it's necessary to completely remove a
> cygwin installation in order to use MinGW and build R.
>
> What I have done to build R from a bash cygwin window under Windows 2000:
>
> (1) put the "tools" directory and the MinGW directories ahead of any cygwin
> directories on the path
> (2) rename the cygwin1.dll that was in the "tools" directory (from Brian
> Ripley's tools.zip) to something like "Xcygwin1.dll" (to avoid cygwin
> conflicts)
>
> I also have ActiveState Perl installed and ahead of the cygwin perl on the
> path (though I have a wrapper for it that translates cygwin paths on the
> command line to windows paths).
>
> This configuration is different from the instructions in
> src/gnuwin32/INSTALL in that I don't use the cygwin1.dll from
> tools.zip. However, since updating some things recently, having
> cygwin1.dll in the tools directory always resulted in the "cygwin1.dll
> conflict" error, even when I changed the PATH to not have any other version
> of cygwin1.dll on it.
>
> This may or may not work for anyone else, but it seems to be working for me
> at the moment: I can build R and the recommended packages from source and
> run the tests.
>
> -- Tony Plate
>
> At Tuesday 11:32 AM 3/16/2004, Jeff D. Hamann wrote:
> >I've been attempting to create a new R package and recently removed the
> >cygwin installation from my machine since R requires the use of the MingW
> >tools for building an R package with C code. However, when I tried to build
> >a source package, I found the following results:
> >
> >
> >* removing junk files
> >* building 'Rconifers_0.7-1.tar.gz'
> >tar: /cygdrive/C/usfs/psw_redding/software/current/Rconifers_0.7-1.tar:
> >Cannot open: No such file or directory
> >tar: Error is not recoverable: exiting now
> >tar: /cygdrive/C/usfs/psw_redding/software/current/Rconifers_0.7-1.tar:
> >Cannot open: No such file or directory
> >tar: Error is not recoverable: exiting now
> >tar: /cygdrive/C/usfs/psw_redding/software/current/Rconifers_0.7-1.tar:
> >Cannot open: No such file or directory
> >tar: Error is not recoverable: exiting now
> >Rconifers_0.7-1.tar: No such file or directory
> >
> >
> >C:\usfs\psw_redding\software\current>
> >
> >which looks like the cygwin path is hard coded into the build script for the
> >rcmd. I found the
> >
> > if($WINDOWS) {
> > ## workaround for paths in Cygwin tar
> > $filepath =~ s+^([A-Za-x]):+/cygdrive/\1+;
> > }
> >
> >in the build script and don't think it needs to be there since you can use
> >the tar utility that comes with mingw, yes? I replaced the previous chunk of
> >code with:
> >
> > if($WINDOWS) {
> > ## workaround for paths in Cygwin tar
> > $filepath =~ s+^([A-Za-x]):+/\1+;
> > }
> >
> >which has solved the problem. I just don't know how to get this into the
> >latest build or release of R?
> >
> >Jeff.
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