R devel - Nov 2008 - Package install problem on Windows (PR#13284)

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

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
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595