Last updated on 2023-06-25 05:53:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.13 | 236.82 | 132.08 | 368.90 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.0.13 | 159.03 | 107.52 | 266.55 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.13 | 417.49 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.13 | 437.93 | ERROR | |||
| r-devel-windows-x86_64 | 0.0.13 | 142.00 | 159.00 | 301.00 | ERROR | |
| r-patched-linux-x86_64 | 0.0.13 | 221.94 | 134.32 | 356.26 | ERROR | |
| r-release-linux-x86_64 | 0.0.13 | 202.09 | 136.52 | 338.61 | ERROR | |
| r-release-macos-arm64 | 0.0.13 | 84.00 | NOTE | |||
| r-release-macos-x86_64 | 0.0.13 | 177.00 | NOTE | |||
| r-release-windows-x86_64 | 0.0.13 | 171.00 | 190.00 | 361.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.0.13 | 77.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.0.13 | 179.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.0.13 | 161.00 | 183.00 | 344.00 | ERROR |
Version: 0.0.13
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000119 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.146 seconds (Warm-up)
Chain 1: 0.206 seconds (Sampling)
Chain 1: 1.352 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.1, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.95 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 2.094 seconds (Warm-up)
Chain 1: 0.422 seconds (Sampling)
Chain 1: 2.516 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.06, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.13
Check: installed package size
Result: NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
doc 1.9Mb
libs 3.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.0.13
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.13
Check: data for non-ASCII characters
Result: NOTE
Note: found 1 marked UTF-8 string
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000124 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.237 seconds (Warm-up)
Chain 1: 0.233 seconds (Sampling)
Chain 1: 1.47 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.1, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.99 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.054 seconds (Warm-up)
Chain 1: 0.269 seconds (Sampling)
Chain 1: 1.323 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.09, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in 'tipsae-Ex.R' failed
The error most likely occurred in:
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000112 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.777 seconds (Warm-up)
Chain 1: 0.218 seconds (Sampling)
Chain 1: 1.995 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.07, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000115 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.585 seconds (Warm-up)
Chain 1: 0.431 seconds (Sampling)
Chain 1: 2.016 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.09, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in ‘tipsae-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00012 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.412 seconds (Warm-up)
Chain 1: 0.459 seconds (Sampling)
Chain 1: 1.871 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.09, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in 'tipsae-Ex.R' failed
The error most likely occurred in:
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000111 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.11 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.893 seconds (Warm-up)
Chain 1: 0.424 seconds (Sampling)
Chain 1: 2.317 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.12, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.0.13
Check: examples
Result: ERROR
Running examples in 'tipsae-Ex.R' failed
The error most likely occurred in:
> ### Name: map
> ### Title: Map Relevant Quantities from a Small Area Model
> ### Aliases: map
>
> ### ** Examples
>
> library(tipsae)
>
> # loading toy dataset
> data("emilia_cs")
>
> # fitting a model
> fit_beta <- fit_sae(formula_fixed = hcr ~ x, data = emilia_cs, domains = "id",
+ type_disp = "var", disp_direct = "vars", domain_size = "n",
+ # MCMC setting to obtain a fast example. Remove next line for reliable results.
+ chains = 1, iter = 300, seed = 0)
SAMPLING FOR MODEL 'global' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.98 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)
Chain 1: Iteration: 30 / 300 [ 10%] (Warmup)
Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)
Chain 1: Iteration: 90 / 300 [ 30%] (Warmup)
Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)
Chain 1: Iteration: 150 / 300 [ 50%] (Warmup)
Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)
Chain 1: Iteration: 180 / 300 [ 60%] (Sampling)
Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)
Chain 1: Iteration: 240 / 300 [ 80%] (Sampling)
Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)
Chain 1: Iteration: 300 / 300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.607 seconds (Warm-up)
Chain 1: 0.404 seconds (Sampling)
Chain 1: 2.011 seconds (Total)
Chain 1:
Warning: The largest R-hat is 1.12, indicating chains have not mixed.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#r-hat
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
>
> # check model diagnostics
> summ_beta <- summary(fit_beta)
Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
>
> # load shapefile of concerned areas
> data("emilia_shp")
>
> # plot the map using model diagnostics and areas shapefile
> map(x = summ_beta,
+ spatial_df = emilia_shp,
+ spatial_id_domains = "NAME_DISTRICT")
Loading required package: sp
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
Warning: `tidy.SpatialPolygonsDataFrame()` was deprecated in broom 1.0.4.
ℹ Please use functions from the sf package, namely `sf::st_as_sf()`, in favor
of sp tidiers.
ℹ The deprecated feature was likely used in the tipsae package.
Please report the issue to the authors.
Error:
! The `region` argument of `tidy.SpatialPolygonsDataFrame()` was
deprecated in broom 1.0.5 and is now defunct.
Backtrace:
▆
1. └─tipsae::map(x = summ_beta, spatial_df = emilia_shp, spatial_id_domains = "NAME_DISTRICT")
2. ├─broom::tidy(spatial_df, region = spatial_id_domains)
3. └─broom:::tidy.SpatialPolygonsDataFrame(spatial_df, region = spatial_id_domains)
4. └─lifecycle::deprecate_stop(when = "1.0.5", what = "tidy.SpatialPolygonsDataFrame(region)")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-oldrel-windows-x86_64