Re: [R-pkg-devel] RData files with identical objects in package
Thanks a lot - for my purpose right now I seem to prosper from not loading
lazy
All best
Troels
-Oprindelig meddelelse-
Fra: peter dalgaard
Sendt: 14. januar 2019 15:17
Til: Troels Ring
Cc: Michael Dewey ; package-develop
Emne: Re: [R-pkg-devel] RData files with identical objects in package
There is (of course) a difference between what is the default for a
(missing) field in DESCRIPTION and what shells like RStudio put into the
field by default...
I don't think there is a discrepancy between what is in the official
documentation and what R and R CMD * actually does.
-pd
> On 14 Jan 2019, at 07:10 , Troels Ring wrote:
>
> Thank you so much! Perhaps it could be mentioned in the official
> documentation on writing R extensions - even if - if I can read
> English - the default is to avoid "lazyData" loading - and "laxyData"
> loading is in some opposition to loading using data() - whereas - if
> we use RStudio, and make an R documentation file for data, we have it
> ending with:
> \examples{
> data(ddd)
> ## maybe str(ddd) ; plot(ddd) ...
> }
> \keyword{datasets}
>
> At the same time as "lazyData" is used default in DESCRIPTION ?
>
> 1.1.6 Data in packages
> The data subdirectory is for data files, either to be made available
> via lazy-loading or for loading using data(). (The choice is made by
> the 'LazyData' field in the DESCRIPTION file: the default is not to do
> so.) It should not be used for other data files needed by the package,
> and the convention has grown up to use directory inst/extdata for such
files.
>
> All best wishes
> Troels
>
>
> -Oprindelig meddelelse-
> Fra: peter dalgaard
> Sendt: 13. januar 2019 22:00
> Til: Troels Ring
> Cc: Michael Dewey ; package-develop
>
> Emne: Re: [R-pkg-devel] RData files with identical objects in package
>
> I think it is illegal if you use the lazyload database, because that
> is indexed by name and contains every object that would be created by
data().
> This creates an obvious issue if two objects share a name.
>
> Once you use the lazyload database, loading the package creates an
> environment which is initially full of promises, one for each object.
> Evaluating one of these makes the actual object appear in the environment.
>
> Using data() causes the corresponding promise(s) to be created in the
> global environment. IIRC, there is a registry that says which objects
> are created by which arguments to data(), but as they are still taken
> from the lazydata database, the last one created with a given name still
wins.
>
> -ps
>
>> On 13 Jan 2019, at 14:13 , Troels Ring wrote:
>>
>> Thanks a lot - I'm sure you are right that I could just use different
>> names but I cannot understand why it could cause problem to have two
>> different well formated .RData files in the /data directory both with
>> an "x" - is that really illegal? I cannot see it stated in the
>> official munual - but it is long (wrting r extensions) -BW Troels
>>
>> -Oprindelig meddelelse-
>> Fra: Michael Dewey
>> Sendt: 13. januar 2019 12:56
>> Til: Troels Ring ; package-develop
>>
>> Emne: Re: [R-pkg-devel] RData files with identical objects in package
>>
>> Dear Troels
>>
>> Perhaps I misunderstand what you are trying to do but would it be
>> possible to put each x and y into a list or a dataframe with
>> different names and then modify your usgae to pull them from there?
>> Then there would be no danger of users getting the wrong x and y
>>
>> Michael
>>
>> On 13/01/2019 08:38, Troels Ring wrote:
>>> Dear friends - I have a package under creation making heavy
>>> calculations on chemical/clinical data and I plan to include as
>>> "examples" the use of some literature data used in my papers. To
>>> illustrate what then occurs, I made two RData files consisting only
>>> of x and y with different values for x and y like
>>>
>>> X <- 100
>>>
>>> Y <- 1000
>>>
>>> save(x,y,file="first.RData")
>>>
>>> and then a new x and y in "second" with x <- 45 and y <- 32
>>>
>>> When I put these in a "data" directory of a new package without
>>> further ado in RStudio
>>>
>>> Ctrl-shift-L
>>>
>>> Ctrl-shift-B
>>>
>>>
>>>
>>> .there is a warning
>>>
>>> * installing *source* package 'try' ...
>>>
>>> ** R
>>>
>>> ** data
>>>
>
Re: [R-pkg-devel] RData files with identical objects in package
There is (of course) a difference between what is the default for a (missing)
field in DESCRIPTION and what shells like RStudio put into the field by
default...
I don't think there is a discrepancy between what is in the official
documentation and what R and R CMD * actually does.
-pd
> On 14 Jan 2019, at 07:10 , Troels Ring wrote:
>
> Thank you so much! Perhaps it could be mentioned in the official
> documentation on writing R extensions - even if - if I can read English -
> the
> default is to avoid "lazyData" loading - and "laxyData" loading is in some
> opposition to loading using data() - whereas - if we use RStudio, and make
> an R documentation file for data, we have it ending with:
> \examples{
> data(ddd)
> ## maybe str(ddd) ; plot(ddd) ...
> }
> \keyword{datasets}
>
> At the same time as "lazyData" is used default in DESCRIPTION ?
>
> 1.1.6 Data in packages
> The data subdirectory is for data files, either to be made available via
> lazy-loading or for loading using data(). (The choice is made by the
> 'LazyData' field in the DESCRIPTION file: the default is not to do so.) It
> should not be used for other data files needed by the package, and the
> convention has grown up to use directory inst/extdata for such files.
>
> All best wishes
> Troels
>
>
> -Oprindelig meddelelse-
> Fra: peter dalgaard
> Sendt: 13. januar 2019 22:00
> Til: Troels Ring
> Cc: Michael Dewey ; package-develop
>
> Emne: Re: [R-pkg-devel] RData files with identical objects in package
>
> I think it is illegal if you use the lazyload database, because that is
> indexed by name and contains every object that would be created by data().
> This creates an obvious issue if two objects share a name.
>
> Once you use the lazyload database, loading the package creates an
> environment which is initially full of promises, one for each object.
> Evaluating one of these makes the actual object appear in the environment.
>
> Using data() causes the corresponding promise(s) to be created in the global
> environment. IIRC, there is a registry that says which objects are created
> by which arguments to data(), but as they are still taken from the lazydata
> database, the last one created with a given name still wins.
>
> -ps
>
>> On 13 Jan 2019, at 14:13 , Troels Ring wrote:
>>
>> Thanks a lot - I'm sure you are right that I could just use different
>> names but I cannot understand why it could cause problem to have two
>> different well formated .RData files in the /data directory both with
>> an "x" - is that really illegal? I cannot see it stated in the
>> official munual - but it is long (wrting r extensions) -BW Troels
>>
>> -Oprindelig meddelelse-
>> Fra: Michael Dewey
>> Sendt: 13. januar 2019 12:56
>> Til: Troels Ring ; package-develop
>>
>> Emne: Re: [R-pkg-devel] RData files with identical objects in package
>>
>> Dear Troels
>>
>> Perhaps I misunderstand what you are trying to do but would it be
>> possible to put each x and y into a list or a dataframe with different
>> names and then modify your usgae to pull them from there? Then there
>> would be no danger of users getting the wrong x and y
>>
>> Michael
>>
>> On 13/01/2019 08:38, Troels Ring wrote:
>>> Dear friends - I have a package under creation making heavy
>>> calculations on chemical/clinical data and I plan to include as
>>> "examples" the use of some literature data used in my papers. To
>>> illustrate what then occurs, I made two RData files consisting only
>>> of x and y with different values for x and y like
>>>
>>> X <- 100
>>>
>>> Y <- 1000
>>>
>>> save(x,y,file="first.RData")
>>>
>>> and then a new x and y in "second" with x <- 45 and y <- 32
>>>
>>> When I put these in a "data" directory of a new package without
>>> further ado in RStudio
>>>
>>> Ctrl-shift-L
>>>
>>> Ctrl-shift-B
>>>
>>>
>>>
>>> .there is a warning
>>>
>>> * installing *source* package 'try' ...
>>>
>>> ** R
>>>
>>> ** data
>>>
>>> *** moving datasets to lazyload DB
>>>
>>> warning: objects 'x', 'y' are created by more than one data call
>>>
>>> ** byte-compile and prepare package for lazy loading
>>>
>>> ** help
>>>
>>> converting help for package 'try'
>
Re: [R-pkg-devel] RData files with identical objects in package
Thank you so much! Perhaps it could be mentioned in the official
documentation on writing R extensions - even if - if I can read English -
the
default is to avoid "lazyData" loading - and "laxyData" loading is in some
opposition to loading using data() - whereas - if we use RStudio, and make
an R documentation file for data, we have it ending with:
\examples{
data(ddd)
## maybe str(ddd) ; plot(ddd) ...
}
\keyword{datasets}
At the same time as "lazyData" is used default in DESCRIPTION ?
1.1.6 Data in packages
The data subdirectory is for data files, either to be made available via
lazy-loading or for loading using data(). (The choice is made by the
'LazyData' field in the DESCRIPTION file: the default is not to do so.) It
should not be used for other data files needed by the package, and the
convention has grown up to use directory inst/extdata for such files.
All best wishes
Troels
-Oprindelig meddelelse-
Fra: peter dalgaard
Sendt: 13. januar 2019 22:00
Til: Troels Ring
Cc: Michael Dewey ; package-develop
Emne: Re: [R-pkg-devel] RData files with identical objects in package
I think it is illegal if you use the lazyload database, because that is
indexed by name and contains every object that would be created by data().
This creates an obvious issue if two objects share a name.
Once you use the lazyload database, loading the package creates an
environment which is initially full of promises, one for each object.
Evaluating one of these makes the actual object appear in the environment.
Using data() causes the corresponding promise(s) to be created in the global
environment. IIRC, there is a registry that says which objects are created
by which arguments to data(), but as they are still taken from the lazydata
database, the last one created with a given name still wins.
-ps
> On 13 Jan 2019, at 14:13 , Troels Ring wrote:
>
> Thanks a lot - I'm sure you are right that I could just use different
> names but I cannot understand why it could cause problem to have two
> different well formated .RData files in the /data directory both with
> an "x" - is that really illegal? I cannot see it stated in the
> official munual - but it is long (wrting r extensions) -BW Troels
>
> -Oprindelig meddelelse-
> Fra: Michael Dewey
> Sendt: 13. januar 2019 12:56
> Til: Troels Ring ; package-develop
>
> Emne: Re: [R-pkg-devel] RData files with identical objects in package
>
> Dear Troels
>
> Perhaps I misunderstand what you are trying to do but would it be
> possible to put each x and y into a list or a dataframe with different
> names and then modify your usgae to pull them from there? Then there
> would be no danger of users getting the wrong x and y
>
> Michael
>
> On 13/01/2019 08:38, Troels Ring wrote:
>> Dear friends - I have a package under creation making heavy
>> calculations on chemical/clinical data and I plan to include as
>> "examples" the use of some literature data used in my papers. To
>> illustrate what then occurs, I made two RData files consisting only
>> of x and y with different values for x and y like
>>
>> X <- 100
>>
>> Y <- 1000
>>
>> save(x,y,file="first.RData")
>>
>> and then a new x and y in "second" with x <- 45 and y <- 32
>>
>> When I put these in a "data" directory of a new package without
>> further ado in RStudio
>>
>> Ctrl-shift-L
>>
>> Ctrl-shift-B
>>
>>
>>
>> .there is a warning
>>
>> * installing *source* package 'try' ...
>>
>> ** R
>>
>> ** data
>>
>> *** moving datasets to lazyload DB
>>
>> warning: objects 'x', 'y' are created by more than one data call
>>
>> ** byte-compile and prepare package for lazy loading
>>
>> ** help
>>
>> converting help for package 'try'
>>
>> *** installing help indices
>>
>> finding HTML links ...hello
html
>>
>> done
>>
>>
>>
>> Now, when I clear the workspace:
>>
>>> ls()
>> character(0)
>>> devtools::load_all(".")
>> Loading try
>>
>> Restarting R session...
>>
>>> library(try)
>>> ls()
>> character(0)
>>> x #-- so even if workspace Is empty x is still kept
>> [1] 45
>>> data(first) # and "first" is not seen x
>> [1] 45
>>
>>
>>
>> x is still present - and y
>>
>>
>>
>> I have been reading and searching in "Writing R extensions" but so
>> far didn't find the clue.
>>
>> Seemingly it is the file w
Re: [R-pkg-devel] RData files with identical objects in package
Thanks a lot - I'm sure you are right that I could just use different names but
I cannot understand why it could cause problem to have two different well
formated .RData files in the /data directory both with an "x" - is that really
illegal? I cannot see it stated in the official munual - but it is long (wrting
r extensions)
-BW
Troels
-Oprindelig meddelelse-
Fra: Michael Dewey
Sendt: 13. januar 2019 12:56
Til: Troels Ring ; package-develop
Emne: Re: [R-pkg-devel] RData files with identical objects in package
Dear Troels
Perhaps I misunderstand what you are trying to do but would it be possible to
put each x and y into a list or a dataframe with different names and then
modify your usgae to pull them from there? Then there would be no danger of
users getting the wrong x and y
Michael
On 13/01/2019 08:38, Troels Ring wrote:
> Dear friends - I have a package under creation making heavy
> calculations on chemical/clinical data and I plan to include as
> "examples" the use of some literature data used in my papers. To
> illustrate what then occurs, I made two RData files consisting only of
> x and y with different values for x and y like
>
> X <- 100
>
> Y <- 1000
>
> save(x,y,file="first.RData")
>
> and then a new x and y in "second" with x <- 45 and y <- 32
>
> When I put these in a "data" directory of a new package without
> further ado in RStudio
>
> Ctrl-shift-L
>
> Ctrl-shift-B
>
>
>
> .there is a warning
>
> * installing *source* package 'try' ...
>
> ** R
>
> ** data
>
> *** moving datasets to lazyload DB
>
> warning: objects 'x', 'y' are created by more than one data call
>
> ** byte-compile and prepare package for lazy loading
>
> ** help
>
>converting help for package 'try'
>
> *** installing help indices
>
> finding HTML links ...hello html
>
> done
>
>
>
> Now, when I clear the workspace:
>
>> ls()
> character(0)
>> devtools::load_all(".")
> Loading try
>
> Restarting R session...
>
>> library(try)
>> ls()
> character(0)
>> x #-- so even if workspace Is empty x is still kept
> [1] 45
>> data(first) # and "first" is not seen x
> [1] 45
>
>
>
> x is still present - and y
>
>
>
> I have been reading and searching in "Writing R extensions" but so far
> didn't find the clue.
>
> Seemingly it is the file with the last name that is assessed - when I rename
> first.RData to "xfile.RData" we get 100 and 1000.
>
> Now and then when running ctrl-shift-L and - B we see
>
>
>
> Attaches package: 'try'
>
> The following objects are masked _by_ '.GlobalEnv':
> x, y
>
>
>
> Sorry for these problems -
>
> BW
> Troels
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
--
Michael
http://www.dewey.myzen.co.uk/home.html
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] RData files with identical objects in package
Thanks a lot - here's is what I get:
A single object matching ‘x’ was found
It was found in the following places
package:try
with value
[1] 100
Now put in the last "xfile.RData" - and
"afile.RData" is still muted
Restarting R session...
> library(try)
> x
[1] 100
> getAnywhere("x")
A single object matching ‘x’ was found
It was found in the following places
package:try
with value
[1] 100
> data(afile)
> x
[1] 100
Whereas we know x in afile.RData is 45
So something is very wrong
Sorry to be so helpless
BW
Troels
-Oprindelig meddelelse-
Fra: Duncan Murdoch
Sendt: 13. januar 2019 12:46
Til: Troels Ring ; package-develop
Emne: Re: [R-pkg-devel] RData files with identical objects in package
On 13/01/2019 3:38 a.m., Troels Ring wrote:
> Dear friends - I have a package under creation making heavy
> calculations on chemical/clinical data and I plan to include as
> "examples" the use of some literature data used in my papers. To
> illustrate what then occurs, I made two RData files consisting only of
> x and y with different values for x and y like
>
> X <- 100
>
> Y <- 1000
>
> save(x,y,file="first.RData")
>
> and then a new x and y in "second" with x <- 45 and y <- 32
>
> When I put these in a "data" directory of a new package without
> further ado in RStudio
>
> Ctrl-shift-L
>
> Ctrl-shift-B
>
>
>
> .there is a warning
>
> * installing *source* package 'try' ...
>
> ** R
>
> ** data
>
> *** moving datasets to lazyload DB
>
> warning: objects 'x', 'y' are created by more than one data call
>
> ** byte-compile and prepare package for lazy loading
>
> ** help
>
>converting help for package 'try'
>
> *** installing help indices
>
> finding HTML links ...hello html
>
> done
>
>
>
> Now, when I clear the workspace:
>
>> ls()
> character(0)
>> devtools::load_all(".")
> Loading try
>
> Restarting R session...
>
>> library(try)
>> ls()
> character(0)
>> x #-- so even if workspace Is empty x is still kept
> [1] 45
>> data(first) # and "first" is not seen x
> [1] 45
>
>
>
> x is still present - and y
>
>
>
> I have been reading and searching in "Writing R extensions" but so far
> didn't find the clue.
>
> Seemingly it is the file with the last name that is assessed - when I rename
> first.RData to "xfile.RData" we get 100 and 1000.
>
> Now and then when running ctrl-shift-L and - B we see
>
>
>
> Attaches package: 'try'
>
> The following objects are masked _by_ '.GlobalEnv':
> x, y
>
Does that every happen when ls() returns character(0)? It seems likely
that you have copies of them in the global workspace, and the message is
correct.
In the earlier situation (ls() *does* return character(0), but x is
still found), you can find where it was found using
getAnywhere("x")
For example,
> x <- 2
> getAnywhere("x")
A single object matching ‘x’ was found
It was found in the following places
.GlobalEnv
with value
[1] 2
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] RData files with identical objects in package
On 13/01/2019 3:38 a.m., Troels Ring wrote:
Dear friends - I have a package under creation making heavy calculations on
chemical/clinical data and I plan to include as "examples" the use of some
literature data used in my papers. To illustrate what then occurs, I made
two RData files consisting only of x and y with different values for x and y
like
X <- 100
Y <- 1000
save(x,y,file="first.RData")
and then a new x and y in "second" with x <- 45 and y <- 32
When I put these in a "data" directory of a new package without further ado
in RStudio
Ctrl-shift-L
Ctrl-shift-B
.there is a warning
* installing *source* package 'try' ...
** R
** data
*** moving datasets to lazyload DB
warning: objects 'x', 'y' are created by more than one data call
** byte-compile and prepare package for lazy loading
** help
converting help for package 'try'
*** installing help indices
finding HTML links ...hello html
done
Now, when I clear the workspace:
ls()
character(0)
devtools::load_all(".")
Loading try
Restarting R session...
library(try)
ls()
character(0)
x #-- so even if workspace Is empty x is still kept
[1] 45
data(first) # and "first" is not seen
x
[1] 45
x is still present - and y
I have been reading and searching in "Writing R extensions" but so far
didn't find the clue.
Seemingly it is the file with the last name that is assessed - when I rename
first.RData to "xfile.RData" we get 100 and 1000.
Now and then when running ctrl-shift-L and - B we see
Attaches package: 'try'
The following objects are masked _by_ '.GlobalEnv':
x, y
Does that every happen when ls() returns character(0)? It seems likely
that you have copies of them in the global workspace, and the message is
correct.
In the earlier situation (ls() *does* return character(0), but x is
still found), you can find where it was found using
getAnywhere("x")
For example,
> x <- 2
> getAnywhere("x")
A single object matching ‘x’ was found
It was found in the following places
.GlobalEnv
with value
[1] 2
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] RData files with identical objects in package
Dear friends - I have a package under creation making heavy calculations on
chemical/clinical data and I plan to include as "examples" the use of some
literature data used in my papers. To illustrate what then occurs, I made
two RData files consisting only of x and y with different values for x and y
like
X <- 100
Y <- 1000
save(x,y,file="first.RData")
and then a new x and y in "second" with x <- 45 and y <- 32
When I put these in a "data" directory of a new package without further ado
in RStudio
Ctrl-shift-L
Ctrl-shift-B
.there is a warning
* installing *source* package 'try' ...
** R
** data
*** moving datasets to lazyload DB
warning: objects 'x', 'y' are created by more than one data call
** byte-compile and prepare package for lazy loading
** help
converting help for package 'try'
*** installing help indices
finding HTML links ...hello html
done
Now, when I clear the workspace:
> ls()
character(0)
> devtools::load_all(".")
Loading try
Restarting R session...
> library(try)
> ls()
character(0)
> x #-- so even if workspace Is empty x is still kept
[1] 45
> data(first) # and "first" is not seen
> x
[1] 45
x is still present - and y
I have been reading and searching in "Writing R extensions" but so far
didn't find the clue.
Seemingly it is the file with the last name that is assessed - when I rename
first.RData to "xfile.RData" we get 100 and 1000.
Now and then when running ctrl-shift-L and - B we see
Attaches package: 'try'
The following objects are masked _by_ '.GlobalEnv':
x, y
Sorry for these problems -
BW
Troels
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
