R devel - Jun 2023 - New behavior when running script in package directory?

Thanks, I checked for .Rprofile and .RData files. They are not present.
I also tried renaming my .emacs.d file in case the problem is due to
my Emacs configuration, but this didn't change anything.

If I go to package/R, start R, and use source('foo.R'), there is no
problem.

But if I use Emacs/ESS to run the script foo.R (with no .emacs.d) I get
an error referring to a temp file /tmp/foo.R!djSwRn, namely

Error in ss(file, echo = visibly, local = local, print.eval = output,  :
  /tmp/foo.R!djSwRn:2:0: unexpected end of input
1: foo <- function(secs) {

Here are the contents of foo.R:
foo <- function(secs) {
  return(secs)
}

What seems to be happening is this. After reading the script into Emacs and
using Ctrl-n to start emacs, R starts, setwd(<path to packageA/R>) is run,
and then the signal package is attached (a dependency of packageA), and
I get the error message. There is no problem when Emacs is used to run
the script in my home directory.

This raises a couple of questions:
1. Why does Emacs/ESS behave differently depending on the
current working directory?
2. Why is the signal package loaded automatically?
3. Why is that temporary file /tmp/foo.R!djSwRn created?
4. What is that function ss() in the error message referring to?
5. Could this be a virus? Under Ubuntu?

Thanks,
Dominick




On Wed, Jun 21, 2023 at 2:17?AM Jan van der Laan <rhelp at eoos.dds.nl>
wrote:
>
> Could there be a .Rprofile or .RData file in the directory where you
> start R? These are run/loaded when you start R when present (with the
> default arguments when starting R).
>
> HTH,
> Jan
>
>
>
> On 20-06-2023 23:38, Dominick Samperi wrote:
> > When I run a script foo.R containing some trivial code in my home
> > directory, via Emacs/ESS, everything works as expected: R
> > starts, and a setwd() command to set the working directory is
> > run automatically before the code in the script is run.
> >
> > But if I copy foo.R to some package/R directory strange
> > things happen. When I use Emacs/ESS to run the script
> > in its new location, R starts, and setwd() is called to set
> > the working directory, but then one or more libraries that the
> > package depends on are loaded, even though I am using no
> > libraries in foo.R.
> >
> > Now consider foo.R that contains the following trivial code:
> > secsToRDateTime <- function(secs) {
> >    day2sec <- 60*60*24
> >    days <- secs/day2sec
> > }
> >
> > When I try to run this from package/R I get...
> >
> > Error in ss(file, echo = visibly, local = local, print.eval = output, 
:
> >    /tmp/gpstime.R!CuSewT:2:0: unexpected end of input
> > 1: secsToRDateTime <- function(secs) {
> >     ^
> >
> > As I said, there are no problems when the script is run from my
> > home directory. This suggests that test scripts can no longer be
> > tested in a package's R directory?
> >
> > Is this true?
> >
> > Thanks,
> > Dominick
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
	[[alternative HTML version deleted]]

If ./Rprofile is not present and ~/.Rprofile is present then R will run the
latter at startup.  Do you have a ~/.Rprofile that defines a ss() function?

-Bill

On Wed, Jun 21, 2023 at 8:50?AM Dominick Samperi <djsamperi at gmail.com>
wrote:
> Thanks, I checked for .Rprofile and .RData files. They are not present.
> I also tried renaming my .emacs.d file in case the problem is due to
> my Emacs configuration, but this didn't change anything.
>
> If I go to package/R, start R, and use source('foo.R'), there is no
> problem.
>
> But if I use Emacs/ESS to run the script foo.R (with no .emacs.d) I get
> an error referring to a temp file /tmp/foo.R!djSwRn, namely
>
> Error in ss(file, echo = visibly, local = local, print.eval = output,  :
>   /tmp/foo.R!djSwRn:2:0: unexpected end of input
> 1: foo <- function(secs) {
>
> Here are the contents of foo.R:
> foo <- function(secs) {
>   return(secs)
> }
>
> What seems to be happening is this. After reading the script into Emacs and
> using Ctrl-n to start emacs, R starts, setwd(<path to packageA/R>) is
run,
> and then the signal package is attached (a dependency of packageA), and
> I get the error message. There is no problem when Emacs is used to run
> the script in my home directory.
>
> This raises a couple of questions:
> 1. Why does Emacs/ESS behave differently depending on the
> current working directory?
> 2. Why is the signal package loaded automatically?
> 3. Why is that temporary file /tmp/foo.R!djSwRn created?
> 4. What is that function ss() in the error message referring to?
> 5. Could this be a virus? Under Ubuntu?
>
> Thanks,
> Dominick
>
>
>
>
> On Wed, Jun 21, 2023 at 2:17?AM Jan van der Laan <rhelp at
eoos.dds.nl>
> wrote:
>
> >
> > Could there be a .Rprofile or .RData file in the directory where you
> > start R? These are run/loaded when you start R when present (with the
> > default arguments when starting R).
> >
> > HTH,
> > Jan
> >
> >
> >
> > On 20-06-2023 23:38, Dominick Samperi wrote:
> > > When I run a script foo.R containing some trivial code in my home
> > > directory, via Emacs/ESS, everything works as expected: R
> > > starts, and a setwd() command to set the working directory is
> > > run automatically before the code in the script is run.
> > >
> > > But if I copy foo.R to some package/R directory strange
> > > things happen. When I use Emacs/ESS to run the script
> > > in its new location, R starts, and setwd() is called to set
> > > the working directory, but then one or more libraries that the
> > > package depends on are loaded, even though I am using no
> > > libraries in foo.R.
> > >
> > > Now consider foo.R that contains the following trivial code:
> > > secsToRDateTime <- function(secs) {
> > >    day2sec <- 60*60*24
> > >    days <- secs/day2sec
> > > }
> > >
> > > When I try to run this from package/R I get...
> > >
> > > Error in ss(file, echo = visibly, local = local, print.eval =
output,
> :
> > >    /tmp/gpstime.R!CuSewT:2:0: unexpected end of input
> > > 1: secsToRDateTime <- function(secs) {
> > >     ^
> > >
> > > As I said, there are no problems when the script is run from my
> > > home directory. This suggests that test scripts can no longer be
> > > tested in a package's R directory?
> > >
> > > Is this true?
> > >
> > > Thanks,
> > > Dominick
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
	[[alternative HTML version deleted]]

On Wed, 21 Jun 2023 11:49:24 -0400
Dominick Samperi <djsamperi at gmail.com> wrote:
> 1. Why does Emacs/ESS behave differently depending on the
> current working directory?
> 2. Why is the signal package loaded automatically?
There's a "package development mode" in ESS:
https://github.com/emacs-ess/ESS/blob/master/lisp/ess-r-package.el

I think that ESS automatically detects that you're inside a package
directory and adjusts its behaviour. This could be related to
"namespaced evaluation"
<https://ess.r-project.org/Manual/ess.html#Namespaced-Evaluation>
("evaluate code in the context of the package being developed", sounds
useful), but I'm not sure about that.
> 3. Why is that temporary file /tmp/foo.R!djSwRn created?
It's probably some part of ESS's mechanism of running R code. I
don't
see where the temporary file name is constructed (maybe a built-in
Emacs function?), but it probably comes from
<https://github.com/emacs-ess/ESS/blob/master/lisp/ess-r-mode.el>.
(Look for calls to .ess.source or .ess.ns_source.)
> 4. What is that function ss() in the error message referring to?
`ss` is a function defined by ESS in order to call R's source() in a
way portable between a very wide range of R versions. (A comment in the
same file says "Should work on *all* versions of R. Do not use _ in
names, nor :: , nor 1L", which includes versions of R considered very
old by now.):

https://github.com/emacs-ess/ESS/blob/master/etc/ESSR/R/.basic.R#L178
> 5. Could this be a virus? Under Ubuntu?
A virus has little reason to be doing this to you. There's much more
money to be made from malicious VSCode extensions than Emacs add-on
packages.

Since you've determined ESS to be causing the difference in the
behaviour, perhaps
<https://ess.r-project.org/index.php?Section=getting%20help> is the way
to go? Unfortunately, I'm not a user of ESS or Emacs, so I'm going off
what information I found on the Web, which may be outdated.

-- 
Best regards,
Ivan