Re: [R-pkg-devel] Problem with package containing spatial data
On 09/02/2023 12:41 p.m., Alexandre Courtiol wrote:
Hi Igor,
I had the same issue using terra rather than sf a couple of weeks ago.
I thought of solving the issue as follow:
1.
store the shapefiles under extdata.
2.
create a function that loads the files:
.build_internal_files <- function() {
## This function should not be called by the user.
## It performs the lazy loading of the data since terra cannot handle
rda files
assign("CountryBorders",terra::vect(system.file("extdata/CountryBorders.shp",package =
"IsoriX")),envir = as.environment("package:IsoriX"))
assign("OceanMask",terra::vect(system.file("extdata/OceanMask.shp",package =
"IsoriX")),envir = as.environment("package:IsoriX"))
}
3. call that function automatically upon attach using |.onAttach()|:
.onAttach <- function(libname,pkgname) {
.build_internal_files()## lazy loading of the internal data
}
It seems to work...
Note that .onAttach() is a standard way of defining a function that is
recognised by R and ran when the package is attached.
Would these files ever be used when your package is not attached, e.g.
through a function imported by a different package? If so, you should
use .onLoad(), not .onAttach().
Duncan Murdoch
++
Alex
On Thu, 9 Feb 2023 at 11:11, Duncan Murdoch > wrote:
On 09/02/2023 3:56 a.m., Ivan Krylov wrote:
> В Wed, 8 Feb 2023 11:32:36 -0300
> Igor L mailto:igorlal...@gmail.com>> пишет:
>
>> spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp')
>>
>> plot(spatial_aisp) # works
>>
>> # Same data from .rda file after use usethis::use_data(spatial_aisp,
>> overwrite = TRUE)
>>
>> x <- ispdata::spatial_aisp
>>
>> plot(x) # do not work
>
> Does this break in a new R session, but start working when you
load the
> sf namespace? I think that your package needs to depend on sf in
order
> for this to work. Specifying it in Imports may be enough to make the
> plot.sf S3 method available to the user.
Specifying a package in the Imports field of DESCRIPTION guarantees
that
it will be available to load, but doesn't load it. Importing something
from it via the NAMESPACE triggers a load, as does executing code like
pkg::fn, or explicitly calling loadNamespace("pkg"), or loading a
package that does one of these things.
> You may encounter other problems if you go this way, like R CMD check
> complaining that you don't use the package you're importing. Loading
> the data from a file on demand would also load the sf namespace and
> thus solve the problem.
Workarounds for the check complaints are discussed here, among other
places: https://stackoverflow.com/a/75384338/2554330
.
Duncan Murdoch
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--
Alexandre Courtiol, www.datazoogang.de
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Re: [R-pkg-devel] CRAN Vignette pdfs garbled in Firefox pdf viewer
On 09/02/2023 10:27 a.m., Mike Blazanin wrote: Hi all, my package gcplyr has several vignettes which, from CRAN, appear garbled when opened with Firefox's pdf viewer ( https://cran.r-project.org/web/packages/gcplyr/index.html). Specifically, instead of regular characters, there are numerous black-outlined white boxes with text inside like "EO 88" or "EO 55". This doesn't occur with the pdf vignettes on Github (https://github.com/mikeblazanin/gcplyr/). This also doesn't occur when CRAN pdfs are opened with Chrome's pdf viewer or Microsoft Edge's pdf viewer, nor when files are downloaded from CRAN and opened with a local pdf viewer. I don't see a problem in Firefox 109.0.1 on a Mac. Maybe the "0.1" is a bug fix? Or maybe I looked in the wrong place. Could you be very specific, i.e. URL, page, line. Duncan Murdoch The issue was documented here: https://github.com/mikeblazanin/gcplyr/issues/112 Anyone have any suggestions for what could be causing this? Thanks! Mike Blazanin [[alternative HTML version deleted]] __ 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 https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Problem with package containing spatial data
Thank you all for your help.
Adam, I followed your suggestion, but I still can't figure out why the data
is only available locally when I run the devtools::load_all() function.
When I install the package from GitHub, the data does not appear (even
using the data() function).
Extdata: https://github.com/igorlaltuf/ispdata/tree/main/inst/extdata
Import: https://github.com/igorlaltuf/ispdata/blob/main/R/spatial_cisp.R
And is there any way to reduce the size of files in gpkg format? The
package increased from 5 to 10 megabytes. I tried to make it smaller with
the function sf::st_write("inst/extdata/spatial_aisp.gpkg", compress =
"deflate", append = F), but the size remained the same.
Thanks again for all the help.
Em qui., 9 de fev. de 2023 às 14:41, Alexandre Courtiol <
alexandre.court...@gmail.com> escreveu:
> Hi Igor,
>
> I had the same issue using terra rather than sf a couple of weeks ago.
>
> I thought of solving the issue as follow:
>
>
>1.
>
>store the shapefiles under extdata.
>2.
>
>create a function that loads the files:
>
> .build_internal_files <- function() {
> ## This function should not be called by the user.
> ## It performs the lazy loading of the data since terra cannot handle rda
> files
> assign("CountryBorders",
> terra::vect(system.file("extdata/CountryBorders.shp", package = "IsoriX")),
> envir = as.environment("package:IsoriX"))
> assign("OceanMask", terra::vect(system.file("extdata/OceanMask.shp",
> package = "IsoriX")), envir = as.environment("package:IsoriX"))
> }
>
>
>1. call that function automatically upon attach using .onAttach():
>
> .onAttach <- function(libname, pkgname) {
> .build_internal_files() ## lazy loading of the internal data
> }
>
> It seems to work...
>
> Note that .onAttach() is a standard way of defining a function that is
> recognised by R and ran when the package is attached.
>
> ++
>
> Alex
>
> On Thu, 9 Feb 2023 at 11:11, Duncan Murdoch
> wrote:
>
>> On 09/02/2023 3:56 a.m., Ivan Krylov wrote:
>> > В Wed, 8 Feb 2023 11:32:36 -0300
>> > Igor L пишет:
>> >
>> >> spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp')
>> >>
>> >> plot(spatial_aisp) # works
>> >>
>> >> # Same data from .rda file after use usethis::use_data(spatial_aisp,
>> >> overwrite = TRUE)
>> >>
>> >> x <- ispdata::spatial_aisp
>> >>
>> >> plot(x) # do not work
>> >
>> > Does this break in a new R session, but start working when you load the
>> > sf namespace? I think that your package needs to depend on sf in order
>> > for this to work. Specifying it in Imports may be enough to make the
>> > plot.sf S3 method available to the user.
>>
>> Specifying a package in the Imports field of DESCRIPTION guarantees that
>> it will be available to load, but doesn't load it. Importing something
>> from it via the NAMESPACE triggers a load, as does executing code like
>> pkg::fn, or explicitly calling loadNamespace("pkg"), or loading a
>> package that does one of these things.
>>
>>
>> > You may encounter other problems if you go this way, like R CMD check
>> > complaining that you don't use the package you're importing. Loading
>> > the data from a file on demand would also load the sf namespace and
>> > thus solve the problem.
>>
>> Workarounds for the check complaints are discussed here, among other
>> places: https://stackoverflow.com/a/75384338/2554330 .
>>
>> Duncan Murdoch
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
>
> --
> Alexandre Courtiol, www.datazoogang.de
>
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[R-pkg-devel] CRAN Vignette pdfs garbled in Firefox pdf viewer
Hi all, my package gcplyr has several vignettes which, from CRAN, appear garbled when opened with Firefox's pdf viewer ( https://cran.r-project.org/web/packages/gcplyr/index.html). Specifically, instead of regular characters, there are numerous black-outlined white boxes with text inside like "EO 88" or "EO 55". This doesn't occur with the pdf vignettes on Github (https://github.com/mikeblazanin/gcplyr/). This also doesn't occur when CRAN pdfs are opened with Chrome's pdf viewer or Microsoft Edge's pdf viewer, nor when files are downloaded from CRAN and opened with a local pdf viewer. The issue was documented here: https://github.com/mikeblazanin/gcplyr/issues/112 Anyone have any suggestions for what could be causing this? Thanks! Mike Blazanin [[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] Problem with package containing spatial data
Hi Igor,
I had the same issue using terra rather than sf a couple of weeks ago.
I thought of solving the issue as follow:
1.
store the shapefiles under extdata.
2.
create a function that loads the files:
.build_internal_files <- function() {
## This function should not be called by the user.
## It performs the lazy loading of the data since terra cannot
handle rda files
assign("CountryBorders",
terra::vect(system.file("extdata/CountryBorders.shp", package =
"IsoriX")), envir = as.environment("package:IsoriX"))
assign("OceanMask", terra::vect(system.file("extdata/OceanMask.shp",
package = "IsoriX")), envir = as.environment("package:IsoriX"))
}
1. call that function automatically upon attach using .onAttach():
.onAttach <- function(libname, pkgname) {
.build_internal_files() ## lazy loading of the internal data
}
It seems to work...
Note that .onAttach() is a standard way of defining a function that is
recognised by R and ran when the package is attached.
++
Alex
On Thu, 9 Feb 2023 at 11:11, Duncan Murdoch
wrote:
> On 09/02/2023 3:56 a.m., Ivan Krylov wrote:
> > В Wed, 8 Feb 2023 11:32:36 -0300
> > Igor L пишет:
> >
> >> spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp')
> >>
> >> plot(spatial_aisp) # works
> >>
> >> # Same data from .rda file after use usethis::use_data(spatial_aisp,
> >> overwrite = TRUE)
> >>
> >> x <- ispdata::spatial_aisp
> >>
> >> plot(x) # do not work
> >
> > Does this break in a new R session, but start working when you load the
> > sf namespace? I think that your package needs to depend on sf in order
> > for this to work. Specifying it in Imports may be enough to make the
> > plot.sf S3 method available to the user.
>
> Specifying a package in the Imports field of DESCRIPTION guarantees that
> it will be available to load, but doesn't load it. Importing something
> from it via the NAMESPACE triggers a load, as does executing code like
> pkg::fn, or explicitly calling loadNamespace("pkg"), or loading a
> package that does one of these things.
>
>
> > You may encounter other problems if you go this way, like R CMD check
> > complaining that you don't use the package you're importing. Loading
> > the data from a file on demand would also load the sf namespace and
> > thus solve the problem.
>
> Workarounds for the check complaints are discussed here, among other
> places: https://stackoverflow.com/a/75384338/2554330 .
>
> Duncan Murdoch
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
--
Alexandre Courtiol, www.datazoogang.de
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Problem with package containing spatial data
On 09/02/2023 3:56 a.m., Ivan Krylov wrote:
В Wed, 8 Feb 2023 11:32:36 -0300
Igor L пишет:
spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp')
plot(spatial_aisp) # works
# Same data from .rda file after use usethis::use_data(spatial_aisp,
overwrite = TRUE)
x <- ispdata::spatial_aisp
plot(x) # do not work
Does this break in a new R session, but start working when you load the
sf namespace? I think that your package needs to depend on sf in order
for this to work. Specifying it in Imports may be enough to make the
plot.sf S3 method available to the user.
Specifying a package in the Imports field of DESCRIPTION guarantees that
it will be available to load, but doesn't load it. Importing something
from it via the NAMESPACE triggers a load, as does executing code like
pkg::fn, or explicitly calling loadNamespace("pkg"), or loading a
package that does one of these things.
You may encounter other problems if you go this way, like R CMD check
complaining that you don't use the package you're importing. Loading
the data from a file on demand would also load the sf namespace and
thus solve the problem.
Workarounds for the check complaints are discussed here, among other
places: https://stackoverflow.com/a/75384338/2554330 .
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Problem with package containing spatial data
В Wed, 8 Feb 2023 11:32:36 -0300
Igor L пишет:
> spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp')
>
> plot(spatial_aisp) # works
>
> # Same data from .rda file after use usethis::use_data(spatial_aisp,
> overwrite = TRUE)
>
> x <- ispdata::spatial_aisp
>
> plot(x) # do not work
Does this break in a new R session, but start working when you load the
sf namespace? I think that your package needs to depend on sf in order
for this to work. Specifying it in Imports may be enough to make the
plot.sf S3 method available to the user.
You may encounter other problems if you go this way, like R CMD check
complaining that you don't use the package you're importing. Loading
the data from a file on demand would also load the sf namespace and
thus solve the problem.
--
Best regards,
Ivan
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