From simon.urbanek at r-project.org  Fri Nov 14 00:47:38 2008
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 13 Nov 2008 18:47:38 -0500
Subject: [Rd] Package install problem on Windows (PR#13284)
In-Reply-To: <491CB41F.503@acm.org>
References: <20081113033503.20E60282EFC1@mail.pubhealth.ku.dk>
	<alpine.LFD.2.00.0811130638370.11928@gannet.stats.ox.ac.uk>
	<491CB41F.503@acm.org>
Message-ID: <AC0B88D2-BA71-49D4-97AE-D3B06BE0BE0A@r-project.org>


On Nov 13, 2008, at 6:11 PM, Tony Plate wrote:

> Thanks for the response.
>
> Are the problems with versioned installs fundamental, or are they  
> just a case of incomplete implementation and rough edges?
> If the latter, would fixes be considered?
>
> I ask because we would find versioned installs very useful in  
> maintaining stable production systems, each of which might run with  
> different versions of various packages, while making it easy to  
> continually develop and refine our packages.  As a point of info,  
> our primary use for versioning would be with our own packages, so we  
> could probably get away without using versioned installs for base or  
> contributed packages.
>

I find it more useful to work with multiple library paths  
(.libPaths()) than versioning packages in the above scenario. We  
usually maintain "stable" package library which is individually  
overridden by additional paths added by the user (e.g. developer  
library for testing) and/or subsystems. The override can also be  
revertive, i.e. a subsystem is free to use older packages in its  
library than the stable library when desired.

Cheers,
S


> However, if the problems with versioned installs are not amenable to  
> the kinds of fixes that users can contribute, then I guess we should  
> look for a different approach.
>
> Suggestions and comments are welcome!  Do many people use versioned  
> installs?
>
> -- Tony Plate (coworker of Lars @ blackmesacapital.com)
>
> Prof Brian Ripley wrote:
>> Installing versioned packages is not supported with namespaces.  I  
>> have suggested from time to time that versioned installs be removed  
>> because of this and other known issues, and recommend that you do  
>> not attempt to use them.
>>
>> On Thu, 13 Nov 2008, lhansen at blackmesacapital.com wrote:
>>
>>> Full_Name: Lars Hansen
>>> Version: 2.8.0
>>> OS: Windows XP Pro x64 SP2
>>> Submission from: (NULL) (71.39.177.36)
>>>
>>>
>>> Hi,
>>>
>>> I have run into a problem using "R CMD INSTALL" with the
>>> "--with-package-versions" option under Windows. It is a bit  
>>> obscure, which could
>>> explain why other people have not run into it.
>>>
>>> We happen to have two packages with almost the same name. One name  
>>> is a subset
>>> of the other. The names are "RtTests" and "RtTestsEG1".  I have no  
>>> problem
>>> installing "RtTests" and many other packages, but run into  
>>> problems installing
>>> "RtTestsEG1". The "RtTestsEG1" package happens to be a simple  
>>> example of how to
>>> use the "RtTests" package, so it depends on "RtTests" (which is  
>>> probably the
>>> problem).
>>>
>>> OK, so this is what happens when I attempt to install "RtTestsEG1":
>>>
>>> $ R CMD INSTALL --with-package-versions --library=$R_LIBS RtTestsEG1
>>>
>>> installing RtTestsEG1 package
>>>
>>> ---------- Making package RtTestsEG1 ------------
>>> adding build stamp to DESCRIPTION
>>> installing R files
>>> preparing package RtTestsEG1 for lazy loading
>>> Loading required package: RtTests
>>> ... [lost of lines removed]
>>> Loading required package: RtTests
>>> Error: evaluation nested too deeply: infinite recursion /
>>> options(expressions=)?
>>> Execution halted
>>> make[2]: *** [lazyload] Error 1
>>> make[1]: *** [all] Error 2
>>> make: *** [pkg-RtTestsEG1] Error 2
>>> *** Installation of RtTestsEG1 failed ***
>>>
>>> After some digging in the Windows makefiles, I found out that  
>>> changing the
>>> locale from "C" to "us" in the "lazyload" target of
>>> $R_HOME/src/gnuwin32/MakePkg, i.e. using "LC_ALL=us" instead of  
>>> "LC_ALL=C",
>>> solves the infinite recursion problem and give an useful message.  
>>> It still fails
>>> but now says:
>>>
>>> Loading required package: RtTests
>>> Warning: S3 methods 'summary.RtTestSetResults',  
>>> 'print.RtTestSetResults',
>>> 'print.RtTestSetResults.summary' were declared in NAMESPACE but  
>>> not found
>>> Error in namespaceExport(ns, exports) :
>>> undefined exports: parseTranscriptFile, compareTranscriptAndOutput
>>> Error: package 'RtTests' could not be loaded
>>> Execution halted
>>>
>>> It is true that RtTests declares the various functions in its name  
>>> space, but
>>> why can they suddenly not be found? If I load RtTests by itself,  
>>> i.e.
>>> library(RtTests), there is no problem.
>>>
>>> I happen to have all this working under Linux, so I tracked down  
>>> the difference.
>>> Turns out that under Linux the equivalent to the "lazyload" target  
>>> is in
>>> "/usr/lib/R/bin/INSTALL" and the difference is in the argument  
>>> passed to
>>> "tools:::makeLazyLoading". Under Linux the full package name with  
>>> version number
>>> is used, i.e. "RtTests_0.1-1". Windows just uses "RtTests".
>>>
>>> So I managed to fix the problem by making Windows use the full  
>>> package name in
>>> the "lazyload" target. I replaced
>>> tools:::makeLazyLoading(\"$(PKG)\"
>>> with
>>> tools:::makeLazyLoading(\"$(notdir $(DPKG))\"
>>>
>>> If I now reinstall "RtTests", I can finally install "RtTestsEG1".
>>>
>>> I must confess, that I do not fully understand exactly what it  
>>> takes to
>>> reproduce this problem. I am guessing that all it takes is a  
>>> package depending
>>> on a versioned package. Maybe the similarity in names introduces a  
>>> problem
>>> because of partial matching. I am guessing that has nothing to do  
>>> with it.
>>>
>>> To sum up the report. I see two problems:
>>>
>>> 1) LC_ALL=C causes infinite recursion. It is as if the C locale  
>>> does not work
>>> under Windows. I do not know what the fix is. It is used many  
>>> places in install
>>> scripts and makefiles. Fixing it in the "lazyload" target is not  
>>> enough. Even
>>> with my change I still get "infinite recursion" and no error  
>>> message if I try to
>>> install "RtTestsEG1" without first installing "RtTests".
>>>
>>> 2) "makeLazyLoading()" in "lazyload" target needs to be called  
>>> with full package
>>> name with embedded version number. I think this is bug under  
>>> Windows and my fix
>>> takes care of it.
>>>
>>> It took some time to figure this out. I am hoping this report will  
>>> save other
>>> people time. I am note sure if I succeeded in describing the  
>>> problem clearly.
>>> Please do not hesitate to ask for clarification.
>>>
>>> Thanks,
>>> Lars Hansen
>>>
>>> P.S.
>>>> sessionInfo()
>>> R version 2.8.0 Patched (2008-10-22 r46776)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] Package install problem on Windows (PR#13284)
Simon Urbanek