From tplate at acm.org  Sat Nov 15 02:01:08 2008
From: tplate at acm.org (Tony Plate)
Date: Fri, 14 Nov 2008 18:01:08 -0700
Subject: [Rd] Package install problem on Windows (PR#13284)
In-Reply-To: <18717.15219.178923.14858@stat.math.ethz.ch>
References: <20081113033503.20E60282EFC1@mail.pubhealth.ku.dk>	<alpine.LFD.2.00.0811130638370.11928@gannet.stats.ox.ac.uk>	<491CB41F.503@acm.org>	<AC0B88D2-BA71-49D4-97AE-D3B06BE0BE0A@r-project.org>
	<18717.15219.178923.14858@stat.math.ethz.ch>
Message-ID: <491E1F54.10809@acm.org>

Thanks to Prof Brian Ripley, Martin Maechler, and Simon Urbanek for the 
very informative responses.  It's good to learn that there is a chance 
that versioned installs will go away -- we will avoid using them.

It's also useful to hear of how others create stable package libraries 
while making continual development possible by using different library 
paths, and by dynamically manipulating library paths.  It makes sense 
for us to take a similar approach.

I guess one could take the multiple-library-path approach to the extreme 
of having a single package in each library, with a library for each 
version, e.g., a version 3.1 of package called xyz could be installed in 
library called "xyz_3.1" (so the path of the package would be 
.../xyz_3.1/xyz, and then one would make a call like library("xyz", 
lib.loc=".../xyz_3.1") to get this version.)  This approach could also 
provide a solution to the challenge (under Windows) of installing a new 
version of package into a library without disturbing running R sessions 
that might have that package attached -- by creating a new library for 
the newly installed package, and dynamically finding the latest library 
prior to attaching packages at the beginning of a session.  Are there 
any potential pitfalls to this approach that we should know about?

-- Tony Plate


Martin Maechler wrote:
>>>>>> "SU" == Simon Urbanek <simon.urbanek at r-project.org>
>>>>>>     on Thu, 13 Nov 2008 18:47:38 -0500 writes:
>>>>>>             
>
>     SU> 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.
>     >> 
>
>     SU> I find it more useful to work with multiple library paths  
>     SU> (.libPaths()) than versioning packages in the above
>     SU> scenario. We usually maintain "stable" package library
>     SU> which is individually overridden by additional paths
>     SU> added by the user (e.g. developer library for testing)
>     SU> and/or subsystems. The override can also be revertive,
>     SU> i.e. a subsystem is free to use older packages in its
>     SU> library than the stable library when desired.
>
> We use the same "technique",
> both using the R_LIBS environment variable, and also amending it
> in an .Rprofile equivalent depending on the version of R (or the
> user), i.e., something like
>
>         libPIns <- function(nlib, beforeLib, msgTxt) {
>           ## Purpose: Insert a directory into .libPaths() *before* another one
>           ## ----------------------------------------------------------------
>           ## Arguments: nlib:  The library directory to insert
>           ##       beforeLib:  (grep-pattern of an) entry in current .libPaths()
>           ##          msgTxt:  optional message text about the insertion
>           ## ----------------------------------------------------------------
>           ## Author: Martin Maechler, 2006
>
>           if(file.exists(nlib)) {
>             if(length({fl <- list.files(nlib); fl[fl != "R.css"]})) {
>               ## only if the library contains any packages :
>               if(!missing(msgTxt) && is.character(msgTxt))
>                 cat("extending .libPaths()", msgTxt,"...\n")
>               ni <- length(iL <- grep(beforeLib, lp <- .libPaths()))
>               if(ni != 1) {
>                 warning(".libPaths() contains ",
>                         if(ni>1) "more" else "no",
>                         " entries matching ",sQuote(beforeLib))
>                 iL <- if(ni > 1) iL[1] else length(lp)
>                 cat("Inserting before position", iL,"..\n")
>               }
>               ii <- 1:length(lp)
>               .libPaths(c(lp[ii < iL], nlib, lp[ii >= iL]))
>             }
>           } else warning(nlib, " is not an existing directory")
>         }
>
> and then somewhere
>
>
>         RVersion <- paste(R.version$major, R.version$minor, sep=".")
>         Rstat <- R.version$status
>         is.Rdevel <- ## Rstat == "beta" ||
>           length(grep("devel", Rstat)) > 0
>         if(is.Rdevel)
>             libPIns(nlib =      file.path(RrootDir,"library-R-devel"),
>                     beforeLib = file.path(RrootDir,"library"),
>                     msgTxt = "for 'R-devel'")
> and other such
>
>         if(.....)
> 	    libPIns(....)
>
> calls.
>
> Martin Maechler, ETH Zurich
>
>
>
>
>
>
>     >> 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
>     >> 
>     >> 
>
> ______________________________________________
>     SU> R-devel at r-project.org mailing list
>     SU> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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>



[Rd] Package install problem on Windows (PR#13284)
Tony Plate