>>>>> "SU" == Simon Urbanek <[EMAIL PROTECTED]>
>>>>> 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, [EMAIL PROTECTED] 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@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>
> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
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