Re: [R-pkg-devel] active bindings in package namespace
Thanks both, this is helpful advice.
On 3/23/19 5:14 PM, Kirill Müller wrote:
> Dear Jack
>
>
> This doesn't answer your question, but I would advise against this design.
>
> - Users do not expect side effects (such as network access) from accessing a
> symbol.
>
> - A function gives you much more flexibility to change the interface later
> on. (Arguments for fetching the data, tokens for API access, ...)
>
> - You already encountered a few quirks that make this an "interesting"
> problem.
>
> A function call only needs a pair of parentheses.
>
>
> Best regards
>
> Kirill
>
>
> On 23.03.19 16:50, Jack O. Wasey wrote:
>> Dear all,
>>
>> I am developing a package which is a front for various online data (icd.data
>> https://github.com/jackwasey/icd.data/ ). The current CRAN version just has
>> lazy-loaded data, but now the package encompasses far more current and
>> historic ICD codes from different countries, these can't be included in the
>> CRAN package even with maximal compression.
>>
>> Other authors have solved this using functions to get the data, with or
>> without a local cache of the retrieved data. No CRAN or other packages I
>> have found after extensive searching use the attractive active binding
>> feature of R.
>>
>> The goal is simple: for the user to refer to the data by its symbol, e.g.,
>> 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be downloaded and
>> parsed transparently (if the user has already granted permission, or after
>> prompt if they haven't).
>>
>> The bindings are set using commands alongside the function definitions in
>> R/*.R .E.g.
>>
>> makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
>> lockBinding("icd10cm_latest", environment())
>>
>> For non-interactive use, CI and CRAN tests, no data should be downloaded,
>> and no cache directory set up without user consent. For interactive use, I
>> ask permission to create a local data cache before downloading data.
>>
>> This works fine... until R CMD check. The following steps seems to 'get' or
>> 'source' everything from the package namespace, which results in triggering
>> the active bindings, and this fails if I am unable to get consent to
>> download data, and want to 'stop' on this error condition.
>> - checking dependencies in R code
>> - checking S3 generic/method consistency
>> - checking foreign function calls
>> - checking R code for possible problems
>>
>> Debugging CI-specific binding bugs is a nightmare because these occur in
>> different R sessions initiated by R CMD check.
>>
>> There may be legitimate reasons to evaluate everything in the namespace, but
>> I've no idea what they are. Incidentally, Rstudio also does 'mget' on the
>> whole package namespace and triggers bindings during autocomplete.
>> https://github.com/rstudio/rstudio/issues/4414
>>
>> Is this something I should raise as an issue with R? Or does anyone have any
>> idea of a sensible approach to this. Currently I have a set of workarounds,
>> but this complicates the code, and has taken an awful lot of time. Does
>> anyone know of any CRAN package which has active bindings in the package
>> namespace?
>>
>> Any ideas appreciated.
>>
>> Jack Wasey
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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Re: [R-pkg-devel] active bindings in package namespace
Dear Jack
This doesn't answer your question, but I would advise against this design.
- Users do not expect side effects (such as network access) from
accessing a symbol.
- A function gives you much more flexibility to change the interface
later on. (Arguments for fetching the data, tokens for API access, ...)
- You already encountered a few quirks that make this an "interesting"
problem.
A function call only needs a pair of parentheses.
Best regards
Kirill
On 23.03.19 16:50, Jack O. Wasey wrote:
Dear all,
I am developing a package which is a front for various online data
(icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
version just has lazy-loaded data, but now the package encompasses far
more current and historic ICD codes from different countries, these
can't be included in the CRAN package even with maximal compression.
Other authors have solved this using functions to get the data, with
or without a local cache of the retrieved data. No CRAN or other
packages I have found after extensive searching use the attractive
active binding feature of R.
The goal is simple: for the user to refer to the data by its symbol,
e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
downloaded and parsed transparently (if the user has already granted
permission, or after prompt if they haven't).
The bindings are set using commands alongside the function definitions
in R/*.R .E.g.
makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding,
environment())
lockBinding("icd10cm_latest", environment())
For non-interactive use, CI and CRAN tests, no data should be
downloaded, and no cache directory set up without user consent. For
interactive use, I ask permission to create a local data cache before
downloading data.
This works fine... until R CMD check. The following steps seems to
'get' or 'source' everything from the package namespace, which results
in triggering the active bindings, and this fails if I am unable to
get consent to download data, and want to 'stop' on this error condition.
- checking dependencies in R code
- checking S3 generic/method consistency
- checking foreign function calls
- checking R code for possible problems
Debugging CI-specific binding bugs is a nightmare because these occur
in different R sessions initiated by R CMD check.
There may be legitimate reasons to evaluate everything in the
namespace, but I've no idea what they are. Incidentally, Rstudio also
does 'mget' on the whole package namespace and triggers bindings
during autocomplete. https://github.com/rstudio/rstudio/issues/4414
Is this something I should raise as an issue with R? Or does anyone
have any idea of a sensible approach to this. Currently I have a set
of workarounds, but this complicates the code, and has taken an awful
lot of time. Does anyone know of any CRAN package which has active
bindings in the package namespace?
Any ideas appreciated.
Jack Wasey
__
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Re: [R-pkg-devel] active bindings in package namespace
On Sat, Mar 23, 2019 at 9:46 PM Jack Wasey wrote:
>
> Thanks for that thought. I do also do this in that package, and the same
> problem exists, since the code in those particular steps of R CMD check also
> calls .onLoad. These steps might even attach the package: the R CMD check
> code in tools is too convoluted for me to unravel, but the result is the
> same: active bindings defined directly in the namespace, or inserted into it
> from .onLoad, get run. .onAttach isn't possible because the namespace is
> sealed already.
cli is on CRAN and checks OK with R CMD check.
> In the example you offer from CLI, the binding is inserted into the "dummy"
> function's immediately enclosing environment, which is AFAIK not the same as
> the package namespace.
It seems to me that it is the same, no?
❯ environment(cli:::dummy)
❯ "symbol" %in% ls(environment(cli:::dummy))
[1] TRUE
G.
> Jack
>
> On 3/23/19 2:14 PM, Gábor Csárdi wrote:
> > Hi, yet another workaround is to create the active binding in the
> > .onLoad() function. Here is an example from the cli package:
> > https://github.com/r-lib/cli/blob/d4756c483f69c2382c27b0b983d0ce7cc7e63763/R/onload.R#L8
> >
> > Gabor
> >
> > On Sat, Mar 23, 2019 at 3:50 PM Jack O. Wasey wrote:
> >>
> >> Dear all,
> >>
> >> I am developing a package which is a front for various online data
> >> (icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
> >> version just has lazy-loaded data, but now the package encompasses far
> >> more current and historic ICD codes from different countries, these
> >> can't be included in the CRAN package even with maximal compression.
> >>
> >> Other authors have solved this using functions to get the data, with or
> >> without a local cache of the retrieved data. No CRAN or other packages I
> >> have found after extensive searching use the attractive active binding
> >> feature of R.
> >>
> >> The goal is simple: for the user to refer to the data by its symbol,
> >> e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
> >> downloaded and parsed transparently (if the user has already granted
> >> permission, or after prompt if they haven't).
> >>
> >> The bindings are set using commands alongside the function definitions
> >> in R/*.R .E.g.
> >>
> >> makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
> >> lockBinding("icd10cm_latest", environment())
> >>
> >> For non-interactive use, CI and CRAN tests, no data should be
> >> downloaded, and no cache directory set up without user consent. For
> >> interactive use, I ask permission to create a local data cache before
> >> downloading data.
> >>
> >> This works fine... until R CMD check. The following steps seems to 'get'
> >> or 'source' everything from the package namespace, which results in
> >> triggering the active bindings, and this fails if I am unable to get
> >> consent to download data, and want to 'stop' on this error condition.
> >> - checking dependencies in R code
> >> - checking S3 generic/method consistency
> >> - checking foreign function calls
> >> - checking R code for possible problems
> >>
> >> Debugging CI-specific binding bugs is a nightmare because these occur in
> >> different R sessions initiated by R CMD check.
> >>
> >> There may be legitimate reasons to evaluate everything in the namespace,
> >> but I've no idea what they are. Incidentally, Rstudio also does 'mget'
> >> on the whole package namespace and triggers bindings during
> >> autocomplete. https://github.com/rstudio/rstudio/issues/4414
> >>
> >> Is this something I should raise as an issue with R? Or does anyone have
> >> any idea of a sensible approach to this. Currently I have a set of
> >> workarounds, but this complicates the code, and has taken an awful lot
> >> of time. Does anyone know of any CRAN package which has active bindings
> >> in the package namespace?
> >>
> >> Any ideas appreciated.
> >>
> >> Jack Wasey
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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Re: [R-pkg-devel] active bindings in package namespace
Thanks for that thought. I do also do this in that package, and the same
problem exists, since the code in those particular steps of R CMD check also
calls .onLoad. These steps might even attach the package: the R CMD check code
in tools is too convoluted for me to unravel, but the result is the same:
active bindings defined directly in the namespace, or inserted into it from
.onLoad, get run. .onAttach isn't possible because the namespace is sealed
already.
In the example you offer from CLI, the binding is inserted into the "dummy"
function's immediately enclosing environment, which is AFAIK not the same as
the package namespace.
Jack
On 3/23/19 2:14 PM, Gábor Csárdi wrote:
> Hi, yet another workaround is to create the active binding in the
> .onLoad() function. Here is an example from the cli package:
> https://github.com/r-lib/cli/blob/d4756c483f69c2382c27b0b983d0ce7cc7e63763/R/onload.R#L8
>
> Gabor
>
> On Sat, Mar 23, 2019 at 3:50 PM Jack O. Wasey wrote:
>>
>> Dear all,
>>
>> I am developing a package which is a front for various online data
>> (icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
>> version just has lazy-loaded data, but now the package encompasses far
>> more current and historic ICD codes from different countries, these
>> can't be included in the CRAN package even with maximal compression.
>>
>> Other authors have solved this using functions to get the data, with or
>> without a local cache of the retrieved data. No CRAN or other packages I
>> have found after extensive searching use the attractive active binding
>> feature of R.
>>
>> The goal is simple: for the user to refer to the data by its symbol,
>> e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
>> downloaded and parsed transparently (if the user has already granted
>> permission, or after prompt if they haven't).
>>
>> The bindings are set using commands alongside the function definitions
>> in R/*.R .E.g.
>>
>> makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
>> lockBinding("icd10cm_latest", environment())
>>
>> For non-interactive use, CI and CRAN tests, no data should be
>> downloaded, and no cache directory set up without user consent. For
>> interactive use, I ask permission to create a local data cache before
>> downloading data.
>>
>> This works fine... until R CMD check. The following steps seems to 'get'
>> or 'source' everything from the package namespace, which results in
>> triggering the active bindings, and this fails if I am unable to get
>> consent to download data, and want to 'stop' on this error condition.
>> - checking dependencies in R code
>> - checking S3 generic/method consistency
>> - checking foreign function calls
>> - checking R code for possible problems
>>
>> Debugging CI-specific binding bugs is a nightmare because these occur in
>> different R sessions initiated by R CMD check.
>>
>> There may be legitimate reasons to evaluate everything in the namespace,
>> but I've no idea what they are. Incidentally, Rstudio also does 'mget'
>> on the whole package namespace and triggers bindings during
>> autocomplete. https://github.com/rstudio/rstudio/issues/4414
>>
>> Is this something I should raise as an issue with R? Or does anyone have
>> any idea of a sensible approach to this. Currently I have a set of
>> workarounds, but this complicates the code, and has taken an awful lot
>> of time. Does anyone know of any CRAN package which has active bindings
>> in the package namespace?
>>
>> Any ideas appreciated.
>>
>> Jack Wasey
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] active bindings in package namespace
Hi, yet another workaround is to create the active binding in the
.onLoad() function. Here is an example from the cli package:
https://github.com/r-lib/cli/blob/d4756c483f69c2382c27b0b983d0ce7cc7e63763/R/onload.R#L8
Gabor
On Sat, Mar 23, 2019 at 3:50 PM Jack O. Wasey wrote:
>
> Dear all,
>
> I am developing a package which is a front for various online data
> (icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
> version just has lazy-loaded data, but now the package encompasses far
> more current and historic ICD codes from different countries, these
> can't be included in the CRAN package even with maximal compression.
>
> Other authors have solved this using functions to get the data, with or
> without a local cache of the retrieved data. No CRAN or other packages I
> have found after extensive searching use the attractive active binding
> feature of R.
>
> The goal is simple: for the user to refer to the data by its symbol,
> e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
> downloaded and parsed transparently (if the user has already granted
> permission, or after prompt if they haven't).
>
> The bindings are set using commands alongside the function definitions
> in R/*.R .E.g.
>
> makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
> lockBinding("icd10cm_latest", environment())
>
> For non-interactive use, CI and CRAN tests, no data should be
> downloaded, and no cache directory set up without user consent. For
> interactive use, I ask permission to create a local data cache before
> downloading data.
>
> This works fine... until R CMD check. The following steps seems to 'get'
> or 'source' everything from the package namespace, which results in
> triggering the active bindings, and this fails if I am unable to get
> consent to download data, and want to 'stop' on this error condition.
> - checking dependencies in R code
> - checking S3 generic/method consistency
> - checking foreign function calls
> - checking R code for possible problems
>
> Debugging CI-specific binding bugs is a nightmare because these occur in
> different R sessions initiated by R CMD check.
>
> There may be legitimate reasons to evaluate everything in the namespace,
> but I've no idea what they are. Incidentally, Rstudio also does 'mget'
> on the whole package namespace and triggers bindings during
> autocomplete. https://github.com/rstudio/rstudio/issues/4414
>
> Is this something I should raise as an issue with R? Or does anyone have
> any idea of a sensible approach to this. Currently I have a set of
> workarounds, but this complicates the code, and has taken an awful lot
> of time. Does anyone know of any CRAN package which has active bindings
> in the package namespace?
>
> Any ideas appreciated.
>
> Jack Wasey
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] active bindings in package namespace
Dear all,
I am developing a package which is a front for various online data
(icd.data https://github.com/jackwasey/icd.data/ ). The current CRAN
version just has lazy-loaded data, but now the package encompasses far
more current and historic ICD codes from different countries, these
can't be included in the CRAN package even with maximal compression.
Other authors have solved this using functions to get the data, with or
without a local cache of the retrieved data. No CRAN or other packages I
have found after extensive searching use the attractive active binding
feature of R.
The goal is simple: for the user to refer to the data by its symbol,
e.g., 'icd10fr2019', or 'icd.data::icd10fr2019', and it will be
downloaded and parsed transparently (if the user has already granted
permission, or after prompt if they haven't).
The bindings are set using commands alongside the function definitions
in R/*.R .E.g.
makeActiveBinding("icd10cm_latest", .icd10cm_latest_binding, environment())
lockBinding("icd10cm_latest", environment())
For non-interactive use, CI and CRAN tests, no data should be
downloaded, and no cache directory set up without user consent. For
interactive use, I ask permission to create a local data cache before
downloading data.
This works fine... until R CMD check. The following steps seems to 'get'
or 'source' everything from the package namespace, which results in
triggering the active bindings, and this fails if I am unable to get
consent to download data, and want to 'stop' on this error condition.
- checking dependencies in R code
- checking S3 generic/method consistency
- checking foreign function calls
- checking R code for possible problems
Debugging CI-specific binding bugs is a nightmare because these occur in
different R sessions initiated by R CMD check.
There may be legitimate reasons to evaluate everything in the namespace,
but I've no idea what they are. Incidentally, Rstudio also does 'mget'
on the whole package namespace and triggers bindings during
autocomplete. https://github.com/rstudio/rstudio/issues/4414
Is this something I should raise as an issue with R? Or does anyone have
any idea of a sensible approach to this. Currently I have a set of
workarounds, but this complicates the code, and has taken an awful lot
of time. Does anyone know of any CRAN package which has active bindings
in the package namespace?
Any ideas appreciated.
Jack Wasey
__
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