R help - Jul 2011 - methods package not loaded by default when using Rscript in R2.13

Dear all,

As the object of this mail suggests, the methods package is not loaded by 
default in R2.13 when using Rscript whereas it is loaded when using an 
interactive session.

An example with the metafor package :

library(metafor)
example(addpoly.rma)

this works in an interaction R shell, but put it in a .R file and use it with 
Rscript, it won't work until you added

library(methods)

One of my colleague had the same issue with other custom R functions (work in 
2.12, not anymore in 2.13 because of the same behavior)

Is this something that was planned or a bug?

Best

Vincent

################################################################

My session info  for the interactive R

################################################################
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C             
 [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=fr_FR.utf8   
 [7] LC_PAPER=fr_FR.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods 
[8] base     

other attached packages:
 [1] metafor_1.6-0    Formula_1.0-0    nlme_3.1-101     gwa_0.0-1       
 [5] genetics_1.3.6   mvtnorm_0.9-9991 MASS_7.3-13      gtools_2.6.2    
 [9] gdata_2.8.2      combinat_0.0-8   rmeta_2.16      

loaded via a namespace (and not attached):
[1] lattice_0.19-26 tools_2.13.0   

#############################################################

the same from Rscript

#############################################################

R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C             
 [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=fr_FR.utf8   
 [7] LC_PAPER=fr_FR.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

other attached packages:
[1] metafor_1.6-0 Formula_1.0-0 nlme_3.1-101 

loaded via a namespace (and not attached):
[1] grid_2.13.0     lattice_0.19-26



________________________________
Dr Vincent Chouraki
Assistant hospitalier universitaire
Service d'épidémiologie régional
CHRU de Lille, France
	[[alternative HTML version deleted]]

Vincent Chouraki wrote:
> 
> Dear all,
> 
> As the object of this mail suggests, the methods package is not loaded by 
> default in R2.13 when using Rscript whereas it is loaded when using an 
> interactive session.
> 
?Rscript  

will tell you why and what you could do to change the default.

Berend

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On Jul 1, 2011, at 12:52 , vincent chouraki wrote:
> Dear all,
> 
> As the object of this mail suggests, the methods package is not loaded by 
> default in R2.13 when using Rscript whereas it is loaded when using an 
> interactive session.
> 
> An example with the metafor package :
> 
> library(metafor)
> example(addpoly.rma)
> 
> this works in an interaction R shell, but put it in a .R file and use it
with
> Rscript, it won't work until you added
> 
> library(methods)
> 
> One of my colleague had the same issue with other custom R functions (work
in
> 2.12, not anymore in 2.13 because of the same behavior)
> 
> Is this something that was planned or a bug?
It's intentional. See help(Rscript) for the reason and the remedies.

-pd

-- 
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