[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

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]]

library(try)
x

getAnywhere("x")

data(afile)
x

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

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]]

On 13 Jan 2019, at 14:13 , Troels Ring <tring at gvdnet.dk> 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 <lists at dewey.myzen.co.uk> 
Sendt: 13. januar 2019 12:56
Til: Troels Ring <tring at gvdnet.dk>; package-develop <r-package-devel at r-project.org>
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]]

-- 
Michael
http://www.dewey.myzen.co.uk/home.html

On 13 Jan 2019, at 14:13 , Troels Ring <tring at gvdnet.dk> 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 <lists at dewey.myzen.co.uk>
Sendt: 13. januar 2019 12:56
Til: Troels Ring <tring at gvdnet.dk>; package-develop 
<r-package-devel at r-project.org>
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

 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]]

--
Michael
http://www.dewey.myzen.co.uk/home.html

On 14 Jan 2019, at 07:10 , Troels Ring <tring at gvdnet.dk> 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 <pdalgd at gmail.com> 
Sendt: 13. januar 2019 22:00
Til: Troels Ring <tring at gvdnet.dk>
Cc: Michael Dewey <lists at dewey.myzen.co.uk>; package-develop
<r-package-devel at r-project.org>
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 <tring at gvdnet.dk> 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 <lists at dewey.myzen.co.uk>
Sendt: 13. januar 2019 12:56
Til: Troels Ring <tring at gvdnet.dk>; package-develop 
<r-package-devel at r-project.org>
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]]

--
Michael
http://www.dewey.myzen.co.uk/home.html

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000
Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

On 14 Jan 2019, at 07:10 , Troels Ring <tring at gvdnet.dk> 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

All best wishes
Troels


-----Oprindelig meddelelse-----
Fra: peter dalgaard <pdalgd at gmail.com>
Sendt: 13. januar 2019 22:00
Til: Troels Ring <tring at gvdnet.dk>
Cc: Michael Dewey <lists at dewey.myzen.co.uk>; package-develop 
<r-package-devel at r-project.org>
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

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

-ps

On 13 Jan 2019, at 14:13 , Troels Ring <tring at gvdnet.dk> 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 <lists at dewey.myzen.co.uk>
Sendt: 13. januar 2019 12:56
Til: Troels Ring <tring at gvdnet.dk>; package-develop 
<r-package-devel at r-project.org>
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]]

--
Michael
http://www.dewey.myzen.co.uk/home.html

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 
2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com