R devel - Apr 2009 - R (2.9.0 rc) CMD INSTALL will leave OOLOCK folder even if installation succeeded

Hi,

since a couple of days ago I see failures when using
R CMD INSTALL -l lib  path-to-src/pkg.tar.gz

This occurs in automated library updating via a shell script and is caused by
the
immediate preceding call to leave an 00LOCK folder
even though the package installation of that call succeeded.
This occurs at random (no obvious/systematic correlation to package name or or
such) and
only for packages where an earlier version has been installed into the same
library location.

e.g.

~/R/hardy$ R-2.9.0/bin/R CMD INSTALL -l R-2.9.x-libs
R-2.9.x-libsSrc/CRAN/feature_1.2.3.tar.gz

...
** building package indices ...
* DONE (feature)

but
~/R/hardy$ ls -al R-2.9.x-libs/00LOCK/feature/
total 0
lrwxrwxrwx 1 XXX epiR 39 Mar 27 05:56 feature ->
/mnt/local/R/hardy/R-2.9.x-libs/feature/

?INSTALL tells me of a workaround via --unsafe or --no-lock but I would prefer
to use the
default incantation.
Any insights what the cause could be?

Regards, Matthias


R version 2.9.0 RC (2009-04-10 r48321)
on Ubuntu hardy

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Matthias Burger                     Project Manager/ Biostatistician
Epigenomics AG    Kleine Praesidentenstr. 1    10178 Berlin, Germany
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ml-it-r-devel at epigenomics.com wrote:
> Hi,
> 
> since a couple of days ago I see failures when using
> R CMD INSTALL -l lib  path-to-src/pkg.tar.gz
> 
> This occurs in automated library updating via a shell script and is caused
by the
> immediate preceding call to leave an 00LOCK folder
> even though the package installation of that call succeeded.
> This occurs at random (no obvious/systematic correlation to package name or
or such) and
> only for packages where an earlier version has been installed into the same
library location.
> 
> e.g.
> 
> ~/R/hardy$ R-2.9.0/bin/R CMD INSTALL -l R-2.9.x-libs
R-2.9.x-libsSrc/CRAN/feature_1.2.3.tar.gz
> 
> ...
> ** building package indices ...
> * DONE (feature)
> 
> but
> ~/R/hardy$ ls -al R-2.9.x-libs/00LOCK/feature/
> total 0
> lrwxrwxrwx 1 XXX epiR 39 Mar 27 05:56 feature ->
/mnt/local/R/hardy/R-2.9.x-libs/feature/
> 
> ?INSTALL tells me of a workaround via --unsafe or --no-lock but I would
prefer to use the
> default incantation.
> Any insights what the cause could be?
> 
> Regards, Matthias
> 
> 
> R version 2.9.0 RC (2009-04-10 r48321)
> on Ubuntu hardy
> 
Not (easily) reproducible for me on r48325 (which only differs from
48321 in the FAQ and package count in internet.Rout.save). So, cannot
possibly fix for 2.9.0 tomorrow. Anything peculiar about your setup
(e.g., networked drive) that might keep the unlink from happening?

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907