R devel - Dec 2010 - Warning message when items of Hmisc are masked by loading a package.

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

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
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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
>
> 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
> -------------------------------
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>


-- 
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
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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

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
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php