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lgnbhl / BFS

🇨🇭Search and Download Data from the Swiss Federal Statistical Office
https://lgnbhl.github.io/BFS
GNU General Public License v3.0
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bfs_get_base_maps error #12

Closed mfpa231 closed 1 year ago

mfpa231 commented 1 year ago

Hello, Thank you for this great tool!

I am unable to get the Maps part to work.

For example when running : switzerland_sf <- bfs_get_base_maps(geom = "suis") I get: Error in if (nchar(dsn) < 1) stop("dsn must point to a source, not an empty string.", : missing value where TRUE/FALSE needed

This prevents the rest of the code in your example from working. Not sure if I'm missing something.

Thanks, MA

Thank for you quick reply!

Session info ─────────────────────────────────────────────────────────── setting value version R version 4.3.1 (2023-06-16) os macOS Monterey 12.6.7 system x86_64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Zurich date 2023-09-13 rstudio 2023.06.0+421 Mountain Hydrangea (desktop) pandoc NA

─ Packages ─────────────────────────────────────────────────────────────── package version date (UTC) lib source anytime 0.3.9 2020-08-27 [1] CRAN (R 4.3.0) backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0) BFS 0.5.3 2023-08-19 [1] CRAN (R 4.3.0) checkmate 2.2.0 2023-04-27 [1] CRAN (R 4.3.0) class 7.3-22 2023-05-03 [1] CRAN (R 4.3.1) classInt 0.4-9 2023-02-28 [1] CRAN (R 4.3.0) cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) curl 5.0.1 2023-06-07 [1] CRAN (R 4.3.0) DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0) dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.3.0) e1071 1.7-13 2023-02-01 [1] CRAN (R 4.3.0) fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0) glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0) gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0) httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0) httr2 0.2.3 2023-05-08 [1] CRAN (R 4.3.0) janitor 2.2.0 2023-02-02 [1] CRAN (R 4.3.0) jsonlite 1.8.5 2023-06-05 [1] CRAN (R 4.3.0) KernSmooth 2.23-21 2023-05-03 [1] CRAN (R 4.3.1) lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0) lubridate 1.9.2 2023-02-10 [1] CRAN (R 4.3.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) plyr 1.8.8 2022-11-11 [1] CRAN (R 4.3.0) proxy 0.4-27 2022-06-09 [1] CRAN (R 4.3.0) purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.0) pxR 0.42.7 2022-11-23 [1] CRAN (R 4.3.0) pxweb 0.16.2 2022-10-31 [1] CRAN (R 4.3.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0) Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0) RJSONIO 1.3-1.8 2023-01-31 [1] CRAN (R 4.3.0) rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0) rstac 0.9.2-4 2023-06-14 [1] CRAN (R 4.3.0) rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0) rvest 1.0.3 2022-08-19 [1] CRAN (R 4.3.0) scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0) selectr 0.4-2 2019-11-20 [1] CRAN (R 4.3.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) sf 1.0-14 2023-07-11 [1] CRAN (R 4.3.0) snakecase 0.11.1 2023-08-27 [1] CRAN (R 4.3.0) stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0) stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyRSS 2.0.7 2023-03-05 [1] CRAN (R 4.3.0) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) timechange 0.2.0 2023-01-11 [1] CRAN (R 4.3.0) units 0.8-3 2023-08-10 [1] CRAN (R 4.3.0) utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0) vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0) withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0) xml2 1.3.4 2023-04-27 [1] CRAN (R 4.3.0) zip 2.3.0 2023-04-17 [1] CRAN (R 4.3.0)

[1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library

─────────

lgnbhl commented 1 year ago

Hello @mfpa231

Thank you for opening the issue and sharing your session info.

I am not sure what it could be. Maybe the function fails to download and get correctly the mapping data files. Could you please run this chuck of code to see if files are accessible with this R code (used in the bfs_get_base_maps()) on your machine:

library(BFS)
library(rappdirs) # install.packages("rappdirs")
library(zip) # install.packages("zip")

# get base map files if not present in cache folder
dir <- rappdirs::user_data_dir(appname = "BFS")
path_base_map <- paste0(dir, "/base_map_", "24025646")

dir.exists(path_base_map)
dir.create(path_base_map, recursive = TRUE, showWarnings = FALSE)

BFS::bfs_download_asset(
  number_asset = "24025646",
  destfile = paste0(path_base_map, ".zip"))

# unzip 
zip::unzip(zipfile = paste0(path_base_map, ".zip"), exdir = path_base_map)

#list all files
files_all <- list.files(path_base_map, recursive = TRUE, full.names = TRUE)

# it should show 10 files
files_all[1:10]
mfpa231 commented 1 year ago

Thank you for your response.

I tried 5 times and each time I got the message 'R session aborted'

lgnbhl commented 1 year ago

Strange. Please run each line of R code and let me know at which line you get the message "R session aborted"?

mfpa231 commented 1 year ago

The code seems to work until this line: zip::unzip(zipfile = paste0(path_base_map, ".zip"), exdir = path_base_map)

philipp-baumann commented 1 year ago 
library(BFS)
library(rappdirs) # install.packages("rappdirs")
library(zip) # install.packages("zip")
#> 
#> Attaching package: 'zip'
#> The following objects are masked from 'package:utils':
#> 
#>     unzip, zip

# get base map files if not present in cache folder
dir <- rappdirs::user_data_dir(appname = "BFS")
path_base_map <- paste0(dir, "/base_map_", "24025646")

dir.exists(path_base_map)
#> [1] TRUE
dir.create(path_base_map, recursive = TRUE, showWarnings = FALSE)

BFS::bfs_download_asset(
  number_asset = "24025646",
  destfile = paste0(path_base_map, ".zip"))
#> [1] "/home/philipp/.local/share/BFS/base_map_24025646.zip"

# unzip 
zip::unzip(zipfile = paste0(path_base_map, ".zip"), exdir = path_base_map)

#list all files
files_all <- list.files(path_base_map, recursive = TRUE, full.names = TRUE)

# it should show 10 files
files_all[1:10]
#>  [1] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd11_ch2007.cpg"
#>  [2] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd11_ch2007.dbf"
#>  [3] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd11_ch2007.prj"
#>  [4] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd11_ch2007.shp"
#>  [5] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd11_ch2007.shx"
#>  [6] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd22_ch2007.cpg"
#>  [7] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd22_ch2007.dbf"
#>  [8] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd22_ch2007.prj"
#>  [9] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd22_ch2007.shp"
#> [10] "/home/philipp/.local/share/BFS/base_map_24025646/2023_GEOM_TK/00_TOPO/K4_flusyyyymmdd/k4flusyyyymmdd22_ch2007.shx"

Created on 2023-09-13 with reprex v2.0.2

philipp-baumann commented 1 year ago 
switzerland_sf <- BFS::bfs_get_base_maps(geom = "suis")
#> Error in nchar(dsn): invalid multibyte string, element 1
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       Ubuntu 22.04.3 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Zurich
#>  date     2023-09-13
#>  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  anytime       0.3.9   2020-08-27 [1] CRAN (R 4.1.3)
#>  BFS           0.5.4   2023-09-13 [1] Github (lgnbhl/BFS@902c825)
#>  class         7.3-20  2022-01-16 [2] CRAN (R 4.1.3)
#>  classInt      0.4-10  2023-09-05 [1] CRAN (R 4.1.3)
#>  cli           3.6.1   2023-03-23 [1] CRAN (R 4.1.3)
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#>  DBI           1.1.3   2022-06-18 [1] RSPM (R 4.1.0)
#>  digest        0.6.33  2023-07-07 [1] CRAN (R 4.1.3)
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#>  e1071         1.7-13  2023-02-01 [1] CRAN (R 4.1.3)
#>  evaluate      0.21    2023-05-05 [1] CRAN (R 4.1.3)
#>  fansi         1.0.4   2023-01-22 [1] CRAN (R 4.1.3)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.1.3)
#>  fs            1.6.3   2023-07-20 [1] CRAN (R 4.1.3)
#>  generics      0.1.3   2022-07-05 [1] CRAN (R 4.1.3)
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#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.2)
#>  rappdirs      0.3.3   2021-01-31 [1] CRAN (R 4.1.2)
#>  Rcpp          1.0.11  2023-07-06 [1] CRAN (R 4.1.3)
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#>  rmarkdown     2.24    2023-08-14 [1] CRAN (R 4.1.3)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.2)
#>  sf            1.0-14  2023-07-11 [1] CRAN (R 4.1.3)
#>  snakecase     0.11.1  2023-08-27 [1] CRAN (R 4.1.3)
#>  stringi       1.7.12  2023-01-11 [1] CRAN (R 4.1.3)
#>  stringr       1.5.0   2022-12-02 [1] CRAN (R 4.1.3)
#>  styler        1.10.2  2023-08-29 [1] CRAN (R 4.1.3)
#>  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.1.3)
#>  tidyRSS       2.0.7   2023-03-05 [1] CRAN (R 4.1.3)
#>  tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.1.3)
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#>  utf8          1.2.3   2023-01-31 [1] CRAN (R 4.1.3)
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#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.3)
#>  xfun          0.40    2023-08-09 [1] CRAN (R 4.1.3)
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#>  yaml          2.3.7   2023-01-23 [1] CRAN (R 4.1.3)
#>  zip           2.3.0   2023-04-17 [1] CRAN (R 4.1.3)
#> 
#>  [1] /home/philipp/R/x86_64-pc-linux-gnu-library/4.1
#>  [2] /opt/R/4.1.3/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Created on 2023-09-13 with reprex v2.0.2

philipp-baumann commented 1 year ago

=> could be an encoding issue, who knows what esri allows in those shapefiles ;-) Might also be some win machine/server doing some non-UTF-8 bad things.

philipp-baumann commented 1 year ago 
r$> traceback()
4: st_read.character(..., quiet = quiet, stringsAsFactors = stringsAsFactors, 
       as_tibble = as_tibble)
3: st_read(..., quiet = quiet, stringsAsFactors = stringsAsFactors, 
       as_tibble = as_tibble)
2: sf::read_sf(file_selected)
1: BFS::bfs_get_base_maps(geom = "suis")
lgnbhl commented 1 year ago

Thank you so much @philipp-baumann !

Yes, could be an encoding issue. I will investigate that.

I have added unit tests, which confirm the bug when using bfs_get_base_maps() on Mac and Linux: https://github.com/lgnbhl/BFS/blob/master/tests/testthat/test-bfs_get_base_maps.R

philipp-baumann commented 1 year ago

Thank you so much @philipp-baumann !

Yes, could be an encoding issue. I will investigate that.

I have added unit tests, which confirm the bug when using bfs_get_base_maps() on Mac and Linux: https://github.com/lgnbhl/BFS/blob/master/tests/testthat/test-bfs_get_base_maps.R

great! yeah that multibyte thing we might do some byte multiplication, but it's known shapefiles pose issues with the encoding.

lgnbhl commented 1 year ago

For the record I tried using the options argument when calling read_sf() at line 86 of "bfs_get_base_maps.R" but it doesn't fix the bug on Mac and Linux:

sf::read_sf(file_selected, options = "ENCODING=UTF-8") #doesn't fix the bug
philipp-baumann commented 1 year ago

For the record I tried using the options argument when calling read_sf() at line 86 of "bfs_get_base_maps.R" but it doesn't fix the bug on Mac and Linux:

sf::read_sf(file_selected, options = "ENCODING=UTF-8") #doesn't fix the bug

I will check this out later today.

philipp-baumann commented 1 year ago

@lgnbhl I found the issue: it is the file path, which contains multibyte strings. When I copy the shape stuff into a clean non-multibyte path, I can read then perfectly well :-)

r$> read_sf("K4suis18480101gf_ch2007Poly.shp")
Simple feature collection with 1 feature and 2 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 2485203 ymin: 1075283 xmax: 2834035 ymax: 1295864
Projected CRS: CH1903+ / LV95
# A tibble: 1 × 3
     id name                                                                               geometry
  <dbl> <chr>                                                                    <MULTIPOLYGON [m]>
1     1 Schweiz/Suisse/Svizzera/Svizra (((2689363 1278165, 2689175 1278875, 2687891 1280259, 26876…

r$> dir()
 [1] "_pkgdown.yml"                        "BFS.Rproj"                          
 [3] "CODE_OF_CONDUCT.md"                  "data"                               
 [5] "data-raw"                            "DESCRIPTION"                        
 [7] "docs"                                "K4suis18480101gf_ch2007Poly.CPG"    
 [9] "K4suis18480101gf_ch2007Poly.dbf"     "K4suis18480101gf_ch2007Poly.prj"    
[11] "K4suis18480101gf_ch2007Poly.qpj"     "K4suis18480101gf_ch2007Poly.shp"    
[13] "K4suis18480101gf_ch2007Poly.shp.xml" "K4suis18480101gf_ch2007Poly.shx"    
[15] "LICENSE"                             "LICENSE.md"                         
[17] "man"                                 "NAMESPACE"                          
[19] "NEWS.md"                             "pkgdown"                            
[21] "R"                                   "README.md"                          
[23] "README.Rmd"                          "tests"                              

r$>

So we can blame Windows, as almost always.

philipp-baumann commented 1 year ago

=> regarding a fix, we need some R internal conversion of the dir tree. Cheers

lgnbhl commented 1 year ago

I just pushed a fix by adding argument useBytes = TRUE in grep() and encoding the selected file as "latin1" using Encoding: https://github.com/lgnbhl/BFS/commit/203b677caacb2ba3c6e99e44f016c3f07114a8a0

This change fixes the bug for Linux. However it seems that it doesn't fix the bug when using Mac: https://github.com/lgnbhl/BFS/actions/runs/6199046399

philipp-baumann commented 1 year ago

I just pushed a fix by adding argument useBytes = TRUE in grep() and encoding the selected file as "latin1" using Encoding: 203b677

This change fixes the bug for Linux. However it seems that it doesn't fix the bug when using Mac: https://github.com/lgnbhl/BFS/actions/runs/6199046399

cool, thanks! but interesting it does not work for MacOS.

philipp-baumann commented 1 year ago

The macOS runners reports a segfault:

 > test_check("BFS")

   *** caught segfault ***
  address 0xffffffff00000000, cause 'memory not mapped'

  Traceback:
   1: zip::unzip(zipfile = paste0(path_base_map, ".zip"), exdir = path_base_map)
   2: bfs_get_base_maps(geom = "suis")
philipp-baumann commented 1 year ago

@lgnbhl maybe I have a weird theory, but is {rappdirs} on MacOS GH runner saving into a path it should not, or respectively is not authorized to do so? hard to believe it is a {zip} bug on MacOS.

philipp-baumann commented 1 year ago

13

lgnbhl commented 1 year ago

@philipp-baumann thank you so much for exploring a fix regarding the unzip() function and {rappdirs}!

Given my limited time this weekend I explored the possibility that the issue on MacOS comes from the use of grep() and list.files(). I found two Stackoverflow discussions that lead me to add "ignore.case = TRUE" in all grep() functions and using fs::dir_ls() instead of list.files():

Unfortunately the issue on MacOS remains. And with these two changes there is also an issue on ubuntu-latest (oldrel-1). I will continue exploring possible fixes...

Thanks again for sharing your testing regarding the unzip() function and {rappdirs} on MacOS!

mfpa231 commented 1 year ago

Thank you both for your time!

lgnbhl commented 1 year ago

@philipp-baumann @mfpa231

I think I fixed the issue! 🎉

My solution is to add "junkpaths = TRUE" when calling unzip() (equivalent to unzip -j), so all the files are extracted in the base folder, therefore avoiding to deal with subfolder name encoding problems. The use of {fs} may also have solved file path issues on MacOS (see https://github.com/lgnbhl/BFS/issues/12#issuecomment-1722297591).

The unit tests are passed on MacOS: https://github.com/lgnbhl/BFS/actions/workflows/R-CMD-check.yaml

@mfpa231 @philipp-baumann could you please let me know if the function works on your side now with BFS version 0.5.5?

devtools::install_github("lgnbhl/BFS") # new BFS version 0.5.5
switzerland_sf <- bfs_get_base_maps(geom = "suis") # should work now
lgnbhl commented 1 year ago

@philipp-baumann thank you so much for you time and your very valuable contributions!

I added your name as a Contributor. Is is okay for you to be named, as I will soon push this new BFS version on CRAN? https://github.com/lgnbhl/BFS/commit/e6abad2499353a112acb7ab91cabefdb9b61437f

philipp-baumann commented 1 year ago

@philipp-baumann @mfpa231

I think I fixed the issue! 🎉

My solution is to add "junkpaths = TRUE" when calling unzip() (equivalent to unzip -j), so all the files are extracted in the base folder, therefore avoiding to deal with subfolder name encoding problems. The use of {fs} may also have solved file path issues on MacOS (see #12 (comment)).

The unit tests are passed on MacOS: https://github.com/lgnbhl/BFS/actions/workflows/R-CMD-check.yaml

@mfpa231 @philipp-baumann could you please let me know if the function works on your side now with BFS version 0.5.5?

devtools::install_github("lgnbhl/BFS") # new BFS version 0.5.5
switzerland_sf <- bfs_get_base_maps(geom = "suis") # should work now

awesome, thanks @lgnbhl for digging deeper and resoving :-) Works for me on Ubuntu 22.04 like in the CI.

philipp-baumann commented 1 year ago

@philipp-baumann thank you so much for you time and your very valuable contributions!

I added your name as a Contributor. Is is okay for you to be named, as I will soon push this new BFS version on CRAN? e6abad2

no worries. sure you can list me as a contributor: 


person("Philipp", "Baumann", , "baumann-philipp@protonmail.com", role = "ctb",
           comment = c(ORCID = "0000-0002-3194-8975"))
lgnbhl commented 1 year ago

The fix has been push to CRAN