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

[Prof Brian Ripley]

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]]
>>
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>


-- 
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