thr3ads.net - R devel - [Rd] Cannot Change Function (PR#14041) [Nov 2009]

If this information is useful, please help other people find it:
Share via:

michael_karsh at earthlink.net

2009-Nov-04 07:50 UTC

[Rd] Cannot Change Function (PR#14041)

Full_Name: Michael Aaron Karsh
Version: 2.8.0
OS: Windows XP
Submission from: (NULL) (75.61.102.255)


Whenever I try changing a function, it keeps coming up with the same error
message.

I have the function
CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log
sum approach
	if(((Im(Tot_log_sum))!=0)|Re(Tot_log_sum)<=log(1/4)/log(2)) {return(0)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(1/4)/log(2))&&((Re(Tot_log_sum))<log(3/4)/log(2)))
{return(1)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>(log(3/4)/log(2)))&&((Re(Tot_log_sum))<log(5/4)/log(2)))
{return(2)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(5/4)/log(2))&&((Re(Tot_log_sum))<log(7/4)/log(2)))
{return(3)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(7/4)/log(2)))
{return(4)}
}

When I try to run it in the loop:
for (j in 1:length(BB_mean_ref)){	# find copy number states (0 for homozygous
deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single amplification,
4 for multiple amplification)
	state_log_sum[j]=CN_state_log_sum(Tot_log_sum[j])
	state_sum_log[j]=CN_state_sum_log(Tot_sum_log[j])
}
I get the error message:
Error in Im(Tot_sum_log) != 0 || Re(Tot_sum_log) <- 2 : 
  could not find function "||<-"

Originally, I had defined the function:
CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log
sum approach
	if(Im(Tot_log_sum)!=0||Re(Tot_log_sum)<-2) return(0)
	if(Im(Tot_log_sum)==0&&Re(Tot_log_sum)>-2)&&Re(Tot_log_sum)<-.4150375)
return(1)
	if(Im(Tot_log_sum)==0&&Re(Tot_log_sum)>-.4150375&&Re(Tot_log_sum)<.3219281)
return(2)
	if(Im(Tot_log_sum)==0&&Re(Tot_log_sum)>.3219281&&Re(Tot_log_sum)<.807355)
return(3)
	if(Im(Tot_log_sum)==0&&Re(Tot_log_sum)>.807355) return(4)
}
When I tried:
for (j in 1:length(BB_mean_ref)){	# find copy number states (0 for homozygous
deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single amplification,
4 for multiple amplification)
	state_log_sum[j]=CN_state_log_sum(Tot_log_sum[j])
	state_sum_log[j]=CN_state_sum_log(Tot_sum_log[j])
}
I get the error message:
Error in Im(Tot_sum_log) != 0 || Re(Tot_sum_log) <- 2 : 
  could not find function "||<-"
I then tried changing the function to:
CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log
sum approach
	if((Im(Tot_log_sum)!=0)||(Re(Tot_log_sum)<-2)) return(0)
	if((Im(Tot_log_sum)==0)&&(Re(Tot_log_sum)>-2))&&(Re(Tot_log_sum)<-.4150375))
return(1)
	if((Im(Tot_log_sum)==0)&&(Re(Tot_log_sum)>-.4150375)&&(Re(Tot_log_sum)<.3219281))
return(2)
	if((Im(Tot_log_sum)==0)&&(Re(Tot_log_sum)>.3219281)&&(Re(Tot_log_sum)<.807355))
return(3)
	if((Im(Tot_log_sum)==0)&&(Re(Tot_log_sum)>.807355)) return(4)
}
I got the same error message.
I then remembered that <- is used to make assignments, when what I wanted to
do
was compare one expression to a negative number.  I then tried changing the
function to:
CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log
sum approach
	if(((Im(Tot_log_sum))!=0)|Re(Tot_log_sum)<=log(1/4)/log(2)) {return(0)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(1/4)/log(2))&&((Re(Tot_log_sum))<log(3/4)/log(2)))
{return(1)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>(log(3/4)/log(2)))&&((Re(Tot_log_sum))<log(5/4)/log(2)))
{return(2)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(5/4)/log(2))&&((Re(Tot_log_sum))<log(7/4)/log(2)))
{return(3)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(7/4)/log(2)))
{return(4)}
}
I got the same error message.

I then tried removing the function using the command:
rm(CN_state_log_sum) and then putting in the function again:
CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state for the log
sum approach
	if(((Im(Tot_log_sum))!=0)|Re(Tot_log_sum)<=log(1/4)/log(2)) {return(0)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(1/4)/log(2))&&((Re(Tot_log_sum))<log(3/4)/log(2)))
{return(1)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>(log(3/4)/log(2)))&&((Re(Tot_log_sum))<log(5/4)/log(2)))
{return(2)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(5/4)/log(2))&&((Re(Tot_log_sum))<log(7/4)/log(2)))
{return(3)}
	if(((Im(Tot_log_sum))==0)&&((Re(Tot_log_sum))>log(7/4)/log(2)))
{return(4)}
}
Same error message.
I tried removing the function again, and then tried saving the new workspace and
the workspace image when I closed R so that it would remember that that function
had been removed when I would open R again. I then opened R again and defined
the same function again. Again, when I tried running it, I got the same error
message.

Stefan Evert

2009-Nov-04 12:40 UTC

head link

[Rd] Cannot Change Function (PR#14041)

What makes you think this is a bug in R?
> Whenever I try changing a function, it keeps coming up with the same  
> error
> message.
>
> I have the function
> CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state  
> for the log
  [...]> }
>
> When I try to run it in the loop:
> for (j in 1:length(BB_mean_ref)){	# find copy number states (0 for  
> homozygous
> deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single  
> amplification,
> 4 for multiple amplification)
> 	state_log_sum[j]=CN_state_log_sum(Tot_log_sum[j])
> 	state_sum_log[j]=CN_state_sum_log(Tot_sum_log[j])
> }
> I get the error message:
> Error in Im(Tot_sum_log) != 0 || Re(Tot_sum_log) <- 2 :
>  could not find function "||<-"
The error message indicates that the problem happens in the function  
CN_state_sum_log() rather than CN_state_log_sum(), so it's hardly  
surprising that changing the latter doesn't have any effect.

My guess: you've go a condition (Re(Tot_sum_log)<-2), which is  
mistaken for the assignment operator "<-" by the R parser. Adding
some
whitespace (Re(Tot_sum_log) < -2) should help both R and human readers  
to make sense of it.

Best,
Stefan

Steven McKinney

2009-Nov-04 21:04 UTC

head link

[Rd] Cannot Change Function (PR#14041)

> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
> project.org] On Behalf Of Stefan Evert
> Sent: Wednesday, November 04, 2009 4:40 AM
> To: michael_karsh at earthlink.net
> Cc: R-bugs at r-project.org; r-devel at stat.math.ethz.ch
> Subject: Re: [Rd] Cannot Change Function (PR#14041)
> 
> What makes you think this is a bug in R?
> 
> > Whenever I try changing a function, it keeps coming up with the same
> > error
> > message.
> >
> > I have the function
> > CN_state_log_sum=function(Tot_log_sum){ #estimate copy number state
> > for the log
>   [...]
> > }
> >
> > When I try to run it in the loop:
> > for (j in 1:length(BB_mean_ref)){	# find copy number states (0 for
> > homozygous
> > deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single
> > amplification,
> > 4 for multiple amplification)
> > 	state_log_sum[j]=CN_state_log_sum(Tot_log_sum[j])
> > 	state_sum_log[j]=CN_state_sum_log(Tot_sum_log[j])
> > }
> > I get the error message:
> > Error in Im(Tot_sum_log) != 0 || Re(Tot_sum_log) <- 2 :
> >  could not find function "||<-"
> 
> The error message indicates that the problem happens in the function
> CN_state_sum_log() rather than CN_state_log_sum(), so it's hardly
> surprising that changing the latter doesn't have any effect.
> 
> My guess: you've go a condition (Re(Tot_sum_log)<-2), which is
> mistaken for the assignment operator "<-" by the R parser.
Adding some
> whitespace (Re(Tot_sum_log) < -2) should help both R and human readers
> to make sense of it.
Adding parentheses around the negative number is the only way to keep
such an expression robustly safe given the various whitespace alterations
that happen as such text passes through different parsers, editors,
mailers, proportional pitch font displays (which can fool human readers) ...

( ( Im(Tot_sum_log) != 0 ) || ( Re(Tot_sum_log) < (-2) ) )

Best

Steven McKinney
> 
> Best,
> Stefan
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

smckinney at bccrc.ca

2009-Nov-04 21:10 UTC

head link

[Rd] Cannot Change Function (PR#14041)

> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
> project.org] On Behalf Of Stefan Evert
> Sent: Wednesday, November 04, 2009 4:40 AM
> To: michael_karsh at earthlink.net
> Cc: R-bugs at r-project.org; r-devel at stat.math.ethz.ch
> Subject: Re: [Rd] Cannot Change Function (PR#14041)
>=20
> What makes you think this is a bug in R?
>=20
> > Whenever I try changing a function, it keeps coming up with the same
> > error
> > message.
> >
> > I have the function
> > CN_state_log_sum=3Dfunction(Tot_log_sum){ #estimate copy number state
> > for the log
>   [...]
> > }
> >
> > When I try to run it in the loop:
> > for (j in 1:length(BB_mean_ref)){	# find copy number states (0 for
> > homozygous
> > deletion, 1 for hemizygous deletion, 2 for neutral, 3 for single
> > amplification,
> > 4 for multiple amplification)
> > 	state_log_sum[j]=3DCN_state_log_sum(Tot_log_sum[j])
> > 	state_sum_log[j]=3DCN_state_sum_log(Tot_sum_log[j])
> > }
> > I get the error message:
> > Error in Im(Tot_sum_log) !=3D 0 || Re(Tot_sum_log) <- 2 :
> >  could not find function "||<-"
>=20
> The error message indicates that the problem happens in the function
> CN_state_sum_log() rather than CN_state_log_sum(), so it's hardly
> surprising that changing the latter doesn't have any effect.
>=20
> My guess: you've go a condition (Re(Tot_sum_log)<-2), which is
> mistaken for the assignment operator "<-" by the R parser.
Adding some
> whitespace (Re(Tot_sum_log) < -2) should help both R and human readers
> to make sense of it.
Adding parentheses around the negative number is the only way to keep
such an expression robustly safe given the various whitespace alterations
that happen as such text passes through different parsers, editors,
mailers, proportional pitch font displays (which can fool human readers) ...

( ( Im(Tot_sum_log) !=3D 0 ) || ( Re(Tot_sum_log) < (-2) ) )

Best

Steven McKinney
>=20
> Best,
> Stefan
>=20
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

R devel - Nov 2009 - Cannot Change Function (PR#14041)

[Rd] Cannot Change Function (PR#14041)

[Rd] Cannot Change Function (PR#14041)

[Rd] Cannot Change Function (PR#14041)

[Rd] Cannot Change Function (PR#14041)