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r-spatial / gstat

Spatial and spatio-temporal geostatistical modelling, prediction and simulation
http://r-spatial.github.io/gstat/
GNU General Public License v2.0
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Problems with Gstat withMarkdown #47

Closed Laurentlsantos closed 5 years ago

Laurentlsantos commented 5 years ago

Dear all,

I am working with Bookdown and I got a problem with the package "gstat".

When I try to knit the chapter, there is a message stating: "package or namespace load failed for 'gstat': package slot missing from signature for generic 'coerce' and classes STFDF, RasterBrick cannot use with duplicate class names".

I have already checked that the package is indeed installed, so I do not know what is wrong.

Thank you for any help in advance.

edzer commented 5 years ago

Maybe reinstall packages raster and spacetime?

Laurentlsantos commented 5 years ago

Hi Edzer! Thanks for your response. I have uninstalled and installed gstat and spacetime many times and It doesn t work to knit the chapter on Bookmark. If I run the code on the "run current chunk" then it runs well. So the code is fine. But when I try to knit the chapter, there is still a problem with the package "gstat". I have installed manually with : install.packages("gstat",dependencies=T) , and then I try library (gstat) and I get the following error: "Error: package or namespace load failed for ‘gstat’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick cannot use with duplicate class names (the package may need to be re-installed)"

Please give me a hint.

edzer commented 5 years ago

What is your sessionInfo()?

Nowosad commented 5 years ago

"package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick"

Wouldn't that suggest some wrong input objects?

Laurentlsantos commented 5 years ago

Hi there! running sessionInfo() I come to know that gstat is not loaded via a namespace. But the package does appear in the pane "packages" (gstat version 2.0-2).

Regarding the code and objects, they are fine since the analysis has been carried on normally on the console. As I mentioned, the problem relates to rendering a chapter with Bookdown.

edzer commented 5 years ago

Please share the output of your sessionInfo() here, and also report the rstudio version you are using.

Laurentlsantos commented 5 years ago

R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] raster_2.9-5 sp_1.3-1

loaded via a namespace (and not attached): [1] zoo_1.8-6 tidyselect_0.2.5 xfun_0.7 purrr_0.3.2
[5] urca_1.3-0 lattice_0.20-38 colorspace_1.4-1 htmltools_0.3.6
[9] viridisLite_0.3.0 yaml_2.2.0 plotly_4.9.0 rlang_0.3.4
[13] pillar_1.4.1 glue_1.3.1 forecast_8.7 TTR_0.23-4
[17] plyr_1.8.4 quantmod_0.4-14 timeDate_3043.102 munsell_0.5.0
[21] gtable_0.3.0 htmlwidgets_1.3 codetools_0.2-16 evaluate_0.14
[25] knitr_1.23 tseries_0.10-47 lmtest_0.9-37 parallel_3.6.0
[29] curl_3.3 xts_0.11-2 Rcpp_1.0.1 scales_1.0.0
[33] jsonlite_1.6 fracdiff_1.4-2 ggplot2_3.1.1 digest_0.6.19
[37] bookdown_0.11 dplyr_0.8.1 grid_3.6.0 quadprog_1.5-7
[41] tools_3.6.0 magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3
[45] crayon_1.3.4 tidyr_0.8.3 pkgconfig_2.0.2 data.table_1.12.2 [49] assertthat_0.2.1 rmarkdown_1.13 httr_1.4.0 rstudioapi_0.10
[53] R6_2.4.0 intervals_0.15.1 nnet_7.3-12 nlme_3.1-139
[57] compiler_3.6.0

edzer commented 5 years ago

Please correct with gstat loaded.

Laurentlsantos commented 5 years ago

R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] raster_2.9-5 sp_1.3-1

loaded via a namespace (and not attached): [1] zoo_1.8-6 tidyselect_0.2.5 xfun_0.7 purrr_0.3.2
[5] urca_1.3-0 lattice_0.20-38 colorspace_1.4-1 htmltools_0.3.6
[9] viridisLite_0.3.0 yaml_2.2.0 plotly_4.9.0 rlang_0.3.4
[13] pillar_1.4.1 glue_1.3.1 forecast_8.7 TTR_0.23-4
[17] plyr_1.8.4 quantmod_0.4-14 timeDate_3043.102 munsell_0.5.0
[21] gtable_0.3.0 htmlwidgets_1.3 codetools_0.2-16 evaluate_0.14
[25] knitr_1.23 tseries_0.10-47 lmtest_0.9-37 parallel_3.6.0
[29] curl_3.3 xts_0.11-2 Rcpp_1.0.1 scales_1.0.0
[33] jsonlite_1.6 fracdiff_1.4-2 ggplot2_3.1.1 digest_0.6.19
[37] bookdown_0.11 dplyr_0.8.1 grid_3.6.0 quadprog_1.5-7
[41] tools_3.6.0 magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3
[45] crayon_1.3.4 tidyr_0.8.3 pkgconfig_2.0.2 data.table_1.12.2 [49] assertthat_0.2.1 rmarkdown_1.13 httr_1.4.0 rstudioapi_0.10
[53] R6_2.4.0 intervals_0.15.1 nnet_7.3-12 nlme_3.1-139
[57] compiler_3.6.0

Laurentlsantos commented 5 years ago

package ‘gstat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\Laurent\AppData\Local\Temp\RtmpWIr3Ez\downloaded_packages

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] raster_2.9-5 sp_1.3-1

loaded via a namespace (and not attached): [1] zoo_1.8-6 tidyselect_0.2.5 xfun_0.7 purrr_0.3.2
[5] urca_1.3-0 lattice_0.20-38 colorspace_1.4-1 htmltools_0.3.6
[9] viridisLite_0.3.0 yaml_2.2.0 plotly_4.9.0 rlang_0.3.4
[13] pillar_1.4.1 glue_1.3.1 forecast_8.7 TTR_0.23-4
[17] plyr_1.8.4 quantmod_0.4-14 timeDate_3043.102 munsell_0.5.0
[21] gtable_0.3.0 htmlwidgets_1.3 codetools_0.2-16 evaluate_0.14
[25] knitr_1.23 tseries_0.10-47 lmtest_0.9-37 parallel_3.6.0
[29] curl_3.3 xts_0.11-2 Rcpp_1.0.1 scales_1.0.0
[33] jsonlite_1.6 fracdiff_1.4-2 ggplot2_3.1.1 digest_0.6.19
[37] bookdown_0.11 dplyr_0.8.1 grid_3.6.0 quadprog_1.5-7
[41] tools_3.6.0 magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3
[45] crayon_1.3.4 tidyr_0.8.3 pkgconfig_2.0.2 data.table_1.12.2 [49] assertthat_0.2.1 rmarkdown_1.13 httr_1.4.0 rstudioapi_0.10
[53] R6_2.4.0 intervals_0.15.1 nnet_7.3-12 nlme_3.1-139
[57] compiler_3.6.0

edzer commented 5 years ago

Yes, but what is sessionInfo() after you give a library(gstat).

Laurentlsantos commented 5 years ago

library(gstat) Error: package or namespace load failed for ‘gstat’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick cannot use with duplicate class names (the package may need to be re-installed)

Laurentlsantos commented 5 years ago

I do install gstat but I am unable to load it

edzer commented 5 years ago

Try loading it in an R session that didn't load anything (also no .RData) on startup.

Laurentlsantos commented 5 years ago

In a completely blank project it works: sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] gstat_2.0-2

loaded via a namespace (and not attached): [1] zoo_1.8-6 compiler_3.6.0 tools_3.6.0 xts_0.11-2
[5] sp_1.3-1 spacetime_1.2-2 yaml_2.2.0 grid_3.6.0
[9] FNN_1.1.3 intervals_0.15.1 lattice_0.20-38

edzer commented 5 years ago

So you can start debugging there: add packages additionally needed one by one, then run your script, and report where and when things break.

Laurentlsantos commented 5 years ago

it works now.

Thank you very much for your support!

andrewmaclachlan commented 4 years ago

What package was causing the issue as i'm also having the same problem

Laurentlsantos commented 4 years ago

Hi Andrew. I followed the recommendation and I debugged the code from zero. I do not remember where the problem comes from.

Challen-Hyman commented 4 years ago

Hi,

I had the same problem after downloading mapview and a few other spatial packages, it looks like now gstat and raster no longer can be loaded together. I just saved the gstat outputs as data frames and reloaded R with raster to continue working.

andrewmaclachlan commented 4 years ago

My solution was just to unload gstat after i used it with: detach("package:gstat", unload=TRUE)

Lvulis commented 3 years ago

My solution was just to unload gstat after i used it with: detach("package:gstat", unload=TRUE)

This solution works, but I found I also need to unload raster from the namespace on R's startup. unloadNamespace('raster')

I also found that calling gstat explicitly (i.e. gstat::fun) works while having raster loaded. Example with some polygon data:

cent <- subset(lakeobjects, perm == 1) %>%
  st_geometry %>%
  st_centroid %>%
  st_sfc %>%
  st_sf
# cent <- st_sf(st_sfc(st_centroid(st_geometry(lakeobjects[, ]))))
cent$area <- subset(lakeobjects, perm == 1)$area

v <- gstat::variogram(area ~ 1, cent)

fv <- gstat::fit.variogram(v, gstat::vgm("Exp"), fit.method = 6)

> fv
  model        psill   range
1   Nug 113270981145     0.0
2   Exp 341807678285 43608.2
Lukpawlik commented 3 years ago

I did have the same problem. After

unloadNamespace('raster') unloadNamespace('terra')

I was able to load gstat.