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 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
>
> __
>
Re: [R-pkg-devel] Getting started with memory debugging
On 14 January 2019 at 09:48, Michael Chirico wrote:
| Hello all,
|
| I'm getting started doing some debugging of memory errors and got stuck
| trying to reproduce the errors found during my CRAN submission process:
|
| https://cran.r-project.org/web/checks/check_results_geohashTools.html
|
| Starting with the clang-ASAN issues, my approach was to try and use the
| rocker/r-devel-san image.
Good idea! I once set this up for a similar need, and then created the
'sanitiziers' package to have a few "known to fail" test cases to make sure
the container was still valid and identifying faults it was supposed to find.
But being busy with a number of other things meant I did not keep up with
this container. So there is no promise it currently reflects what CRAN tests
for.
Winston built another (comprehensive !!) set of images over at this repo:
https://github.com/wch/r-debug
These are more current -- but fundamentally they have the same exact flaw:
CRAN does their thing, and someone has to catch up. Deep down, that really
is a silly game. We'd be (much) better off if the CRAN testbeds were truly
reproducible, and I had meant to write something up suggestion something
around that idea. It hasn't happened.
So here you are.
| Launching with the package directory mounted via:
|
| docker run --rm -it -v
| /Users/michael.chirico/github/geohashTools/:/home/docker/geohashTools
| rocker/r-devel-san /bin/bash
|
| Building required libraries:
|
| apt-get update
| apt-get install libgdal-dev libudunits2-dev
|
| Then installing my Imports/Suggests:
|
| Rscript -e "install.packages(c('Rcpp', 'sp', 'sf', 'testthat', 'mockery'))"
|
| Now attempting to reproduce the memory errors:
|
| cd /home/docker/geohashTools
| RD CMD build .
| RD CMD check geohashTools_0.2.0.tar.gz
|
| But this is check is successful (I was hoping it'd fail)... I assume the
| problem is from the last few steps. The manual says:
|
| >
| > It requires code to have been compiled and linked with -fsanitize=address
|
| But I'm not sure how to enforce this (I assumed it was being handled by how
| RD binary is built but I didn't notice any compilation output from R CMD
| build .
I am a little out of sync with your package here. Maybe it "merely" requires
that the library you reinstalled also rebuilds with -fsanitize=address which
you could ensure, I'd hope, via PKG_CPPFLAGS and/or editing of its src/Makevars.
Because that is essentially it: you do need *all* of
- R itself
- the package you wanted
- and its dependencies
to be built consistently for SAN/ASAN with the very settings CRAN uses.
Which are "documented" in a README somewhere on some site. I think it is
worthwhile having a conversation about how we can do one step better than
that. I would be happy to help, but a little constrained on free time and
cannot lead this. Can you, or someone else?
Dirk
|
| Any help on getting started here would be appreciated :)
| Michael Chirico
|
| PS the source can be found at https://github.com/MichaelChirico/geohashTools
|
| [[alternative HTML version deleted]]
|
| __
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Getting started with memory debugging
Hello all,
I'm getting started doing some debugging of memory errors and got stuck
trying to reproduce the errors found during my CRAN submission process:
https://cran.r-project.org/web/checks/check_results_geohashTools.html
Starting with the clang-ASAN issues, my approach was to try and use the
rocker/r-devel-san image.
Launching with the package directory mounted via:
docker run --rm -it -v
/Users/michael.chirico/github/geohashTools/:/home/docker/geohashTools
rocker/r-devel-san /bin/bash
Building required libraries:
apt-get update
apt-get install libgdal-dev libudunits2-dev
Then installing my Imports/Suggests:
Rscript -e "install.packages(c('Rcpp', 'sp', 'sf', 'testthat', 'mockery'))"
Now attempting to reproduce the memory errors:
cd /home/docker/geohashTools
RD CMD build .
RD CMD check geohashTools_0.2.0.tar.gz
But this is check is successful (I was hoping it'd fail)... I assume the
problem is from the last few steps. The manual says:
>
> It requires code to have been compiled and linked with -fsanitize=address
But I'm not sure how to enforce this (I assumed it was being handled by how
RD binary is built but I didn't notice any compilation output from R CMD
build .
Any help on getting started here would be appreciated :)
Michael Chirico
PS the source can be found at https://github.com/MichaelChirico/geohashTools
[[alternative HTML version deleted]]
__
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 - 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]]
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