Re: [R] Tidying up code - Warning message: deparse may be incomplete
On 28/08/2008 10:46 AM, Marie Pierre Sylvestre wrote:
Dear R users,
I am currently writing a R package and to do so I am following the
guidelines in manual 'Writing R extensions'.
In Section 3.1, it is suggested to tidy up the code using a file
containing the following:
options(keep.source = FALSE)
source(myfuns..R)
dump(ls(all = TRUE), file = new.myfuns.R)
I have done this for my own packages and although it runs, I get several
warnings of the type:
Warning message:
In dump(ls(all = TRUE), file = PermAlgo.R) : deparse may be incomplete
I am clueless as to what this means.
Even if I try to tidy only one function from my code, I get the warning.
E.g. the file lala.R contains only this:
partialHazards - function(t, v, covArray, betas){ exp( covArray[v,t,]
%*% betas ) }
the file tidylala.R contains:
options(keep.source = FALSE)
source(lala.R)
dump(ls(all = TRUE), file = newlala.R)
On Linux I run:
R --vanilla tidylala.R
Then I obtain:
Warning message:
In dump(ls(all = TRUE), file = newlala.R) : deparse may be incomplete
The file newlala.R looks like this:
`partialHazards` -
function (t, v, covArray, betas)
{
exp(covArray[v, t, ] %*% betas)
}
What does the warning mean? Can I simply ignore it?
I've now taken a look, and this really was a bug. source() was
partially ignoring options(keep.source = FALSE), and this confused
dump(). I've fixed it in R-patched.
I've also clarified the advice about tidying up code, by adding a
warning that following it will delete all of your comments. I think
you're better off writing it in a tidy way in the first place, or using
a smart editor to reformat it. R retains enough information to write a
code prettifier that preserves comments, but I don't know of one.
Duncan Murdoch
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tidying up code - Warning message: deparse may be incomplete
DM == Duncan Murdoch [EMAIL PROTECTED]
on Fri, 29 Aug 2008 08:36:12 -0400 writes:
DM On 28/08/2008 10:46 AM, Marie Pierre Sylvestre wrote:
Dear R users,
I am currently writing a R package and to do so I am following the
guidelines in manual 'Writing R extensions'.
In Section 3.1, it is suggested to tidy up the code using a file
containing the following:
options(keep.source = FALSE)
source(myfuns..R)
dump(ls(all = TRUE), file = new.myfuns.R)
I have done this for my own packages and although it runs, I get several
warnings of the type:
Warning message:
In dump(ls(all = TRUE), file = PermAlgo.R) : deparse may be incomplete
I am clueless as to what this means.
Even if I try to tidy only one function from my code, I get the warning.
E.g. the file lala.R contains only this:
partialHazards - function(t, v, covArray, betas){ exp( covArray[v,t,]
%*% betas ) }
the file tidylala.R contains:
options(keep.source = FALSE)
source(lala.R)
dump(ls(all = TRUE), file = newlala.R)
On Linux I run:
R --vanilla tidylala.R
Then I obtain:
Warning message:
In dump(ls(all = TRUE), file = newlala.R) : deparse may be incomplete
The file newlala.R looks like this:
`partialHazards` -
function (t, v, covArray, betas)
{
exp(covArray[v, t, ] %*% betas)
}
What does the warning mean? Can I simply ignore it?
DM I've now taken a look, and this really was a bug. source() was
DM partially ignoring options(keep.source = FALSE), and this confused
DM dump(). I've fixed it in R-patched.
DM I've also clarified the advice about tidying up code, by adding a
DM warning that following it will delete all of your comments. I think
DM you're better off writing it in a tidy way in the first place, or using
DM a smart editor to reformat it. R retains enough information to write a
DM code prettifier that preserves comments, but I don't know of one.
I strongly agree with your last paragraph,
and I have always thought that we should recommend using
R-aware editors rather than dump() nowadays ...
but then I thought that I've been biased at all times, being a
co-developer of ESS, authoring its M-x ess-fix-miscellaneous
(and more), and also the author of a (non public) Emacs lisp
file called 'R-stylepolice.el' as early as in 1999.
Martin Maechler
DM Duncan Murdoch
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Re: [R] Tidying up code - Warning message: deparse may be incomplete
Martin Maechler wrote: I strongly agree with your last paragraph, and I have always thought that we should recommend using R-aware editors rather than dump() nowadays ... but then I thought that I've been biased at all times, being a co-developer of ESS, authoring its M-x ess-fix-miscellaneous (and more), and also the author of a (non public) Emacs lisp file called 'R-stylepolice.el' as early as in 1999. BTW: Has there been any progress on turning the highlighting _off_ in iESS and transcript mode? The highlighted for and in make me crazy... -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tidying up code - Warning message: deparse may be incomplete
Dear R users,
I am currently writing a R package and to do so I am following the
guidelines in manual 'Writing R extensions'.
In Section 3.1, it is suggested to tidy up the code using a file
containing the following:
options(keep.source = FALSE)
source(myfuns..R)
dump(ls(all = TRUE), file = new.myfuns.R)
I have done this for my own packages and although it runs, I get several
warnings of the type:
Warning message:
In dump(ls(all = TRUE), file = PermAlgo.R) : deparse may be incomplete
I am clueless as to what this means.
Even if I try to tidy only one function from my code, I get the warning.
E.g. the file lala.R contains only this:
partialHazards - function(t, v, covArray, betas){ exp( covArray[v,t,]
%*% betas ) }
the file tidylala.R contains:
options(keep.source = FALSE)
source(lala.R)
dump(ls(all = TRUE), file = newlala.R)
On Linux I run:
R --vanilla tidylala.R
Then I obtain:
Warning message:
In dump(ls(all = TRUE), file = newlala.R) : deparse may be incomplete
The file newlala.R looks like this:
`partialHazards` -
function (t, v, covArray, betas)
{
exp(covArray[v, t, ] %*% betas)
}
What does the warning mean? Can I simply ignore it?
thanks,
MP
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tidying up code - Warning message: deparse may be incomplete
On 28/08/2008 10:46 AM, Marie Pierre Sylvestre wrote:
Dear R users,
I am currently writing a R package and to do so I am following the
guidelines in manual 'Writing R extensions'.
In Section 3.1, it is suggested to tidy up the code using a file
containing the following:
options(keep.source = FALSE)
source(myfuns..R)
dump(ls(all = TRUE), file = new.myfuns.R)
I have done this for my own packages and although it runs, I get several
warnings of the type:
Warning message:
In dump(ls(all = TRUE), file = PermAlgo.R) : deparse may be incomplete
I am clueless as to what this means.
Even if I try to tidy only one function from my code, I get the warning.
E.g. the file lala.R contains only this:
partialHazards - function(t, v, covArray, betas){ exp( covArray[v,t,]
%*% betas ) }
the file tidylala.R contains:
options(keep.source = FALSE)
source(lala.R)
dump(ls(all = TRUE), file = newlala.R)
On Linux I run:
R --vanilla tidylala.R
Then I obtain:
Warning message:
In dump(ls(all = TRUE), file = newlala.R) : deparse may be incomplete
The file newlala.R looks like this:
`partialHazards` -
function (t, v, covArray, betas)
{
exp(covArray[v, t, ] %*% betas)
}
What does the warning mean? Can I simply ignore it?
The warning means that you may have lost some information, i.e. sourcing
newlala.R won't produce the same thing as sourcing lala.R. I think in
your case, there's no loss, so it's a bug, but I don't have time to
track down why you're getting it.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
