[R-SIG-Mac] packages, R-patched and RC [Was: Importing Excel files]

peter dalgaard pdalgd at gmail.com
Wed Jun 20 12:20:26 CEST 2012 

On Jun 19, 2012, at 23:29 , Prof Brian Ripley wrote:

> On 19/06/2012 17:35, Simon Urbanek wrote:
>> On Jun 19, 2012, at 5:36 AM, peter dalgaard wrote:
>> 
>>> 
>>> On Jun 19, 2012, at 01:16 , Colstat wrote:
>>> 
>>>> I think the error says it
>>>> "package Œgdata‚ was built under R version 2.15.1"
>>>> and you have R 2.5.10.
>>>> 
>>>> Update your R first, let me know if it doesn't work.
>>> 
>>> 2.15.1 is announced for Friday... I think it's a bit of a glitch that CRAN is already automatically providing packages for it, but you are of course more than welcome to test the prereleases (from http://R.research.att.com/).
>>> 
>>> I suppose that this comes about from building packages with R-patched, which transitions directly into the prereleases for the next version.
>>> 
>> 
>> Yes, this is a side-effect of that. I wonder what we can do about it - I used to build packages with released versions only, but then people complained that patched had fixes for some things they needed...
> 
> We could simply not update the version of R-patched used during the beta/RC periods: they are after all only about 10 days.
> 

Yes, that would handle the formal issue of the version number conflict. 

However, there's a deeper issue which got highlighted by the identical() debacle in April-June: It seems that we can't guarantee ABI compatibility throughout the R-branch series (e.g., everything labeled 2.15.x). We try to ensure that the modified versions of R will run packages built with a previous version, but the other way around might not work. If that sort of thing happens in R-patched, midway between releases, then users could find themselves blocked from installing packages until they update to R-patched, which could be undesirable in corporate or educational settings.

Some R-core deliberations might be called for...



>> Cheers,
>> Simon
>> 
>> 
>>> 
>>>> 
>>>> On Mon, Jun 18, 2012 at 5:28 PM, Victoria Xiao<victoriayxiao at gmail.com>wrote:
>>>> 
>>>>> Exactly. Every time I try to load it from the package manager, the check
>>>>> mark in the check box vanishes and the status goes back to 'not loaded'. At
>>>>> the same time, I get this error message:
>>>>> 
>>>>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>>>>> there is no package called Œgtools‚
>>>>> In addition: Warning message:
>>>>> package Œgdata‚ was built under R version 2.15.1
>>>>> Error: package/namespace load failed for Œgdata‚
>>>>> It's very perplexing. Would uninstalling and reinstalling gdata help at
>>>>> all?
>>>>> 
>>>>> Thanks again.
>>>>> 
>>>>> On Mon, Jun 18, 2012 at 2:23 PM, Colstat<colstat at gmail.com>  wrote:
>>>>> 
>>>>>> Looking at your output, and if you are using package 'gdata'.
>>>>>> Then under "Other attached packages" of your output
>>>>>> 
>>>>>> you don't have,
>>>>>>> gdata_2.6.2
>>>>>> 
>>>>>> Are you sure you have loaded the package correctly?  It doesn't look like
>>>>>> it.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Mon, Jun 18, 2012 at 5:15 PM, Victoria Xiao<victoriayxiao at gmail.com>wrote:
>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Jun 18, 2012 at 2:13 PM, Colstat<colstat at gmail.com>  wrote:
>>>>>>> 
>>>>>>>> Hi Victor,
>>>>>>>> could you type sessionInfo() in R terminal and paste here what you got?
>>>>>>>> 
>>>>>>>> On Mon, Jun 18, 2012 at 5:06 PM, Victoria Xiao<victoriayxiao at gmail.com
>>>>>>>>> wrote:
>>>>>>>> 
>>>>>>>>> Hi all,
>>>>>>>>> 
>>>>>>>>> I'm trying to figure out how to import Excel files into R. I'm running
>>>>>>>>> Mac
>>>>>>>>> 10.6, and so far I've tried the xlsx and gdata packages; both gave
>>>>>>>>> error
>>>>>>>>> messages.
>>>>>>>>> 
>>>>>>>>> For the xlsx package, here is what I got:
>>>>>>>>> 
>>>>>>>>>> library(xlsx)
>>>>>>>>>> project.source = "/Users/vicki/Desktop/R/test/kdReport.xls" #change
>>>>>>>>> the
>>>>>>>>> path and file name here
>>>>>>>>>> PIGF.elisa.dat = read.xlsx (file=project.source, 1, header=T)
>>>>>>>>> Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,
>>>>>>>>> : java.lang.IllegalArgumentException: Your InputStream was neither an
>>>>>>>>> OLE2
>>>>>>>>> stream, nor an OOXML stream
>>>>>>>>> 
>>>>>>>>> For the gdata package, it said that gtools was required; when gtools
>>>>>>>>> package was attempted to load, this error message resulted:
>>>>>>>>> 
>>>>>>>>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>>>>>>>>> there is no package called Œgtools‚
>>>>>>>>> In addition: Warning message:
>>>>>>>>> package Œgdata‚ was built under R version 2.15.1
>>>>>>>>> Error: package/namespace load failed for Œgdata‚
>>>>>>>>> 
>>>>>>>>> Does anyone know how to resolve either of these error messages, or if
>>>>>>>>> there
>>>>>>>>> are better packages to interact with Excel files in R on a Mac? Thanks
>>>>>>>>> so
>>>>>>>>> much.
>>>>>>>>> 
>>>>>>>>> Sincerely,
>>>>>>>>> Victoria Xiao
>>>>>>>>> 
>>>>>>>>>      [[alternative HTML version deleted]]
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>> R-SIG-Mac at r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> sessionInfo()
>>>>>>> R version 2.15.0 (2012-03-30)
>>>>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>>>>>> 
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>> 
>>>>>>> attached base packages:
>>>>>>> [1] splines   stats     graphics  grDevices utils     datasets  methods
>>>>>>> [8] base
>>>>>>> 
>>>>>>> other attached packages:
>>>>>>> [1] epicalc_2.14.1.6 xlsx_0.4.2       xlsxjars_0.4.0   rJava_0.9-3
>>>>>>> [5] rj_1.1.0-4       nnet_7.3-1       MASS_7.3-17      survival_2.36-12
>>>>>>> [9] foreign_0.8-49
>>>>>>> 
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] tools_2.15.0
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>> 	[[alternative HTML version deleted]]
>>>> 
>>>> _______________________________________________
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>>> 
>>> --
>>> 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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> _______________________________________________
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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

-- 
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

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