[Rd] Warning message when items of Hmisc are masked by loading a package.

[peter dalgaard]

On Dec 21, 2010, at 17:03 , Joris Meys wrote:

> I know the masking message is standard behaviour. It is the warning mesage
> 
>> Warning message:
>> In identical(get(., i), get(., lib.pos)) : ignoring non-pairlist attributes
> 
> that puzzles me. And that's something I noticed only in 2.12.1
> 

It's a buglet in identical and somewhat older than that (as old as CHARSXP cacheing, I'd expect). It was fixed in R-devel a couple of weeks ago, but not deemed important enough to break code freeze for 2.12.1.

-pd

> Cheers
> Joris
> 
> 
> On Tue, Dec 21, 2010 at 4:59 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>> I thought that was standard behavior? It's been happening when I load Hmisc
>> since the dawn of time (or 3 years anyway.... back to R 2.8.0 at least.)
>>  Hmisc masks some function(s) in survival.
>> 
>> #----------
>> Attaching package: 'Hmisc'
>> 
>> The following object(s) are masked from 'package:survival':
>> 
>>    untangle.specials
>> 
>> The following object(s) are masked from 'package:base':
>> 
>>    format.pval, round.POSIXt, trunc.POSIXt, units
>> 
>> 
>> Attaching package: 'rms'
>> 
>> The following object(s) are masked from 'package:survival':
>> 
>>    Surv
>> #---------------
>> 
>> It only seems fair that if you later mask functions in Hmisc that you also
>> get a warning:
>> 
>> 
>> #----------------
>>> library (reshape)
>> Loading required package: plyr
>> 
>> Attaching package: 'plyr'
>> 
>> The following object(s) are masked from 'package:Hmisc':
>> 
>>    is.discrete, summarize
>> 
>> 
>> Attaching package: 'reshape'
>> 
>> The following object(s) are masked from 'package:plyr':
>> 
>>    round_any
>> 
>> #-----------------
>> 
>> --
>> David.
>> 
>> 
>> 
>> On Dec 21, 2010, at 8:51 AM, Joris Meys wrote:
>> 
>>> PS : This did not happen in R 2.12.0, it just occured when I installed
>>> the new R version today.
>>> Cheers
>>> Joris
>>> 
>>> On Tue, Dec 21, 2010 at 2:50 PM, Joris Meys <jorismeys at gmail.com> wrote:
>>>> 
>>>> I've noticed that I get a warning message every time a package masks
>>>> some functions from Hmisc. The warning message says :
>>>> 
>>>> Warning message:
>>>> In identical(get(., i), get(., lib.pos)) : ignoring non-pairlist
>>>> attributes
>>>> 
>>>> This happens with eg:
>>>> library(plyr)
>>>> library(xtable)
>>>> 
>>>> I think I've seen this passing by before, but I'm not sure any more.
>>>> Just thought I'd mention it.
>>>> Cheers
>>>> Joris
>>>> 
>>>>> R.Version()
>>>> 
>>>> $platform
>>>> [1] "i386-pc-mingw32"
>>>> 
>>>> $arch
>>>> [1] "i386"
>>>> 
>>>> $os
>>>> [1] "mingw32"
>>>> 
>>>> $system
>>>> [1] "i386, mingw32"
>>>> 
>>>> $status
>>>> [1] ""
>>>> 
>>>> $major
>>>> [1] "2"
>>>> 
>>>> $minor
>>>> [1] "12.1"
>>>> 
>>>> $year
>>>> [1] "2010"
>>>> 
>>>> $month
>>>> [1] "12"
>>>> 
>>>> $day
>>>> [1] "16"
>>>> 
>>>> $`svn rev`
>>>> [1] "53855"
>>>> 
>>>> $language
>>>> [1] "R"
>>>> 
>>>> $version.string
>>>> [1] "R version 2.12.1 (2010-12-16)"
>>>> 
>>>>> Sys.info()
>>>> 
>>>>    sysname      release      version     nodename      machine
>>>>  login         user
>>>>  "Windows"      "7 x64" "build 7600"  "JFMEYS-PC"        "x86"
>>>> "Joris"      "Joris"
>>>> 
>>>> --
>>>> Joris Meys
>>>> Statistical consultant
>> 
>> David Winsemius, MD
>> West Hartford, CT
>> 
>> 
> 
> 
> 
> -- 
> Joris Meys
> Statistical consultant
> 
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
> 
> tel : +32 9 264 59 87
> Joris.Meys at Ugent.be
> -------------------------------
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-- 
Peter Dalgaard
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