From pdalgd at gmail.com  Thu Apr  3 15:39:00 2014
From: pdalgd at gmail.com (peter dalgaard)
Date: Thu, 3 Apr 2014 15:39:00 +0200
Subject: [Rd] Timezone warnings on package install in R-alpha
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Thanks to Brian. Yet another thing that zoomed by without me really noticing.

However, I'd like to be sure that it isn't a "make dist" issue. We do seem to ship the correct files in src/extra/tzone, but could you please check Brian's suggestion about TZDIR possibly being set incorrectly?

-pd

On 03 Apr 2014, at 14:47 , Jon Clayden <jon.clayden at gmail.com> wrote:

> Many thanks, Prof Ripley. The "--without-internal-tzcode" option does indeed resolve the problem.
> 
> Regards,
> Jon
> 
> 
> On 3 April 2014 13:38, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> On 03/04/2014 13:27, peter dalgaard wrote:
> I'm seeing nothing of the sort with the nightly build of 3.1.0RC, also on 10.9.2. This is a plain-vanilla Xcode+ancillaries build as per Simon's instructions (I think):
> 
> pd$ more config.site
> r_arch=${r_arch:=x86_64}
> CC="gcc -arch $r_arch"
> CXX="g++ -arch $r_arch"
> F77="gfortran -arch $r_arch"
> FC="gfortran -arch $r_arch"
> OBJC="gcc -arch $r_arch"
> with_blas="-framework vecLib"
> with_lapack=yes
> 
> so either something is up specifically with gcc-4.8, or you managed to hose your time zone data base somehow (/usr/share/zoneinfo, I suppose).
> 
> More likely the one shipping with R, since --with-internal-tzcode is the default on OS X [*].  Setting TZDIR incorrectly would do this:
> 
> > Sys.time()
> [1] "2014-04-03 12:37:01 GMT"
> Warning messages:
> 1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'Europe/London'
> 2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
> 3: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
> 
> when I do that.
> 
> You could try --without-internal-tzcode.
> 
> [*] Although x86_64 OS X has a 64-bit time_t it seems to have a 32-bit time-zone database and so wraps around.
> 
> 
> 
> - Peter D.
> 
> On 03 Apr 2014, at 13:24 , Jon Clayden <jon.clayden at gmail.com> wrote:
> 
> For what it's worth, this issue persists in R-rc_2014-04-02_r65358.
> 
> Regards,
> Jon
> 
> 
> On 24 March 2014 10:40, Jon Clayden <jon.clayden at gmail.com> wrote:
> 
> Dear all,
> 
> As of the current R alpha release, I'm seeing timezone-related warnings on
> installing any package (including the recommended ones), which I haven't
> seen before. For example,
> 
> [~/Documents/Source/R-alpha]$ bin/R CMD INSTALL ~/git/tractor/lib/reportr
> * installing to library '/Users/jon/Documents/Source/R-alpha/library'
> * installing *source* package 'reportr' ...
> Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'Europe/London'
> Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
> Warning in as.POSIXlt.POSIXct(x, tz) :
>   unknown timezone 'America/New_York'
> Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
> Warning in as.POSIXlt.POSIXct(x, tz) :
>   unknown timezone 'America/New_York'
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (reportr)
> 
> This is R-alpha r65266, built from source on OS X 10.9.2 using gcc 4.8.2.
> I ran configure with
> 
> ./configure --with-blas="-framework Accelerate" --with-lapack
> --with-system-zlib --enable-memory-profiling
> --with-tcl-config=/System/Library/Frameworks/Tcl.framework/tclConfig.sh
> --with-tk-config=/System/Library/Frameworks/Tk.framework/tkConfig.sh
> CC=gcc-4.8 CXX=g++-4.8 OBJC=clang F77=gfortran-4.8 FC=gfortran-4.8
> CPPFLAGS="-D__ACCELERATE__" CFLAGS="-mtune=native -g -O2"
> CXXFLAGS="-mtune=native -g -O2" FFLAGS="-mtune=native -g -O2"
> FCFLAGS="-mtune=native -g -O2"
> 
> Session info is
> 
> R version 3.1.0 alpha (2014-03-23 r65266)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> I see some related material in the NEWS, but no indication that these
> warnings are expected. I hope this report is helpful.
> 
> All the best,
> Jon
> 
> 
> 
>         [[alternative HTML version deleted]]
> 
> ______________________________________________
> 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
> 

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] Timezone warnings on package install in R-alpha
peter dalgaard