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rbind error when using add_row on sf objects #1748

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bart1 opened this issue Nov 25, 2022 · 3 comments
Open

rbind error when using add_row on sf objects #1748

bart1 opened this issue Nov 25, 2022 · 3 comments

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@bart1
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bart1 commented Nov 25, 2022

I'm not sure if this is an error of the vctrs implementation in sf or a problem in vtrcs, as the suggestion is to report it here I'll do that first. The error occurs when 0 rows are added to an sf data.frame (as part of code where the number of rows added is variable).

require(sf)
require(dplyr)
g<-data.frame(a=1, x=1,y=4)
add_row(g, a=numeric())
#>   a x y
#> 1 1 1 4
g<-st_as_sf(data.frame(a=1, x=1,y=4), coords = 2:3)
add_row(g, a=6)
#> Simple feature collection with 2 features and 1 field (with 1 geometry empty)
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: 1 ymin: 4 xmax: 1 ymax: 4
#> CRS:           NA
#>   a    geometry
#> 1 1 POINT (1 4)
#> 2 6 POINT EMPTY
add_row(g, a=numeric())
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 3 instead of 1.
#> ℹ In file 'c.c' at line 412.
#> ℹ This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://https://tidyverse.org/help/>) and the full backtrace.

#> Backtrace:
#>     ▆
#>  1. ├─tibble::add_row(g, a = numeric())
#>  2. │ └─tibble:::rbind_at(.data, df, pos)
#>  3. │   └─vctrs::vec_rbind(old, new)
#>  4. └─rlang:::stop_internal_c_lib(...)
#>  5.   └─rlang::abort(message, call = call, .internal = TRUE, .frame = frame)
sessionInfo()
#> R version 4.2.2 Patched (2022-11-10 r83330)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] dplyr_1.0.10 sf_1.0-9    
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.9         pillar_1.8.1       compiler_4.2.2     highr_0.9         
#>  [5] class_7.3-20       R.methodsS3_1.8.2  R.utils_2.12.0     tools_4.2.2       
#>  [9] digest_0.6.29      evaluate_0.17      lifecycle_1.0.3    tibble_3.1.8      
#> [13] R.cache_0.16.0     pkgconfig_2.0.3    rlang_1.0.6        reprex_2.0.2      
#> [17] cli_3.4.1          DBI_1.1.3          rstudioapi_0.14    yaml_2.3.6        
#> [21] xfun_0.33          fastmap_1.1.0      e1071_1.7-12       withr_2.5.0       
#> [25] styler_1.7.0       stringr_1.4.1      knitr_1.40         generics_0.1.3    
#> [29] fs_1.5.2           vctrs_0.5.1        tidyselect_1.2.0   grid_4.2.2        
#> [33] classInt_0.4-8     glue_1.6.2         R6_2.5.1           winch_0.0.11      
#> [37] fansi_1.0.3        rmarkdown_2.17     purrr_0.3.5        magrittr_2.0.3    
#> [41] units_0.8-0        htmltools_0.5.3    assertthat_0.2.1   KernSmooth_2.23-20
#> [45] utf8_1.2.2         stringi_1.7.8      proxy_0.4-27       R.oo_1.25.0

Created on 2022-11-25 with reprex v2.0.2
@DanChaltiel
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Same here with pckg_vrs columns so it might be a wider problem:

Sys.setenv(LANGUAGE="en")
a=tibble::tibble(y=package_version("1.0.0"))
b=tibble::tibble(x=character(0))
dplyr::bind_rows(a, b)
#> Warning in y[bad] <- rep.int(list(integer()), length(bad)): number of items to
#> replace is not a multiple of replacement length
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 3 instead of 1.
#> i In file 'c.c' at line 414.
#> i This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.
#> Backtrace:
#>     x
#>  1. +-dplyr::bind_rows(a, b)
#>  2. | \-vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())
#>  3. \-rlang:::stop_internal_c_lib(...)
#>  4.   \-rlang::abort(message, call = call, .internal = TRUE, .frame = frame)

Created on 2023-05-05 with reprex v2.0.2

Oddly, I don't get the Warning in y[bad] output outside of reprex.

@avsdev-cw
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Also seeing this, however for me it is caused by binding 2 tibbles where only 1 has a geometry column and either tibble is empty:

  df1 <- tibble::tibble(
    ref = c("143_2", "143_2", "143_2", "143_2", "143_2"),
    block = c("206/3", "217/8", "206/3", "206/3", "217/8"),
    date = structure(c(19448, 19449, 19449, 19450, 19451), class = "Date")
  )

  df2 <- tibble::tibble(
    ref = character(0),
    latitude = numeric(0),
    longitude = numeric(0),
    date = structure(numeric(0), class = "Date"),
    geometry = sf::st_sfc(crs = 4326)
  )

  dplyr::bind_rows(df1, df2)
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 6 instead of 5.
#> ℹ In file 'c.c' at line 412.
#> ℹ This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.

Created on 2023-07-21 by the reprex package (v2.0.0)

  df1 <- tibble::tibble(
    ref = c("143_2", "143_2", "143_2", "143_2", "143_2"),
    block = c("206/3", "217/8", "206/3", "206/3", "217/8"),
    date = structure(c(19448, 19449, 19449, 19450, 19451), class = "Date"),
    geometry = sf::st_sfc(sf::st_polygon(), crs = 4326)
  )

  df2 <- tibble::tibble(
    ref = character(0),
    latitude = numeric(0),
    longitude = numeric(0),
    date = structure(numeric(0), class = "Date")
  )

  dplyr::bind_rows(df1, df2)
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 7 instead of 5.
#> ℹ In file 'c.c' at line 412.
#> ℹ This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.

Created on 2023-07-21 by the reprex package (v2.0.0)

  df1 <- tibble::tibble(
    ref = c("143_2", "143_2", "143_2", "143_2", "143_2"),
    block = c("206/3", "217/8", "206/3", "206/3", "217/8"),
    date = structure(c(19448, 19449, 19449, 19450, 19451), class = "Date"),
    geometry = sf::st_sfc(sf::st_polygon(), crs = 4326)
  )

  df2 <- tibble::tibble(
    ref = character(0),
    latitude = numeric(0),
    longitude = numeric(0),
    date = structure(numeric(0), class = "Date"),
    geometry = sf::st_sfc(crs = 4326)
  )

  dplyr::bind_rows(df1, df2)
#> # A tibble: 5 × 6
#>   ref   block date            geometry latitude longitude
#>   <chr> <chr> <date>     <POLYGON [°]>    <dbl>     <dbl>
#> 1 143_2 206/3 2023-04-01         EMPTY       NA        NA
#> 2 143_2 217/8 2023-04-02         EMPTY       NA        NA
#> 3 143_2 206/3 2023-04-02         EMPTY       NA        NA
#> 4 143_2 206/3 2023-04-03         EMPTY       NA        NA
#> 5 143_2 217/8 2023-04-04         EMPTY       NA        NA

Created on 2023-07-21 by the reprex package (v2.0.0)

@avsdev-cw avsdev-cw mentioned this issue Aug 14, 2023
Open
@DavisVaughan DavisVaughan mentioned this issue Nov 6, 2023
Open
@njtierney
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I get this error when binding a tibble with some rows to a spatial data frame with 0 rows:

library(tibble)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(sf)
#> Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
dat <- tibble(x = 1:5, y = 11:15)
dat
#> # A tibble: 5 × 2
#>       x     y
#>   <int> <int>
#> 1     1    11
#> 2     2    12
#> 3     3    13
#> 4     4    14
#> 5     5    15
dat_sf <- st_sf(geometry=st_sfc())
dat_sf
#> Simple feature collection with 0 features and 0 fields
#> Bounding box:  xmin: NA ymin: NA xmax: NA ymax: NA
#> CRS:           NA
#> [1] geometry
#> <0 rows> (or 0-length row.names)
bind_rows(dat, dat_sf)
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 6 instead of 5.
#> ℹ In file 'c.c' at line 414.
#> ℹ This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.
bind_rows(dat_sf, dat)
#> Error in `vec_rbind()`:
#> ! `c()` method returned a vector of unexpected size 6 instead of 5.
#> ℹ In file 'c.c' at line 414.
#> ℹ This is an internal error that was detected in the vctrs package.
#>   Please report it at <https://github.com/r-lib/vctrs/issues> with a reprex (<https://tidyverse.org/help/>) and the full backtrace.
bind_rows(dat_sf, dat_sf)
#> Simple feature collection with 0 features and 0 fields
#> Bounding box:  xmin: NA ymin: NA xmax: NA ymax: NA
#> CRS:           NA
#> [1] geometry
#> <0 rows> (or 0-length row.names)
bind_rows(dat, dat)
#> # A tibble: 10 × 2
#>        x     y
#>    <int> <int>
#>  1     1    11
#>  2     2    12
#>  3     3    13
#>  4     4    14
#>  5     5    15
#>  6     1    11
#>  7     2    12
#>  8     3    13
#>  9     4    14
#> 10     5    15

Created on 2024-05-02 with reprex v2.1.0

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       macOS Sonoma 14.3.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Australia/Brisbane
#>  date     2024-05-02
#>  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  class         7.3-22  2023-05-03 [2] CRAN (R 4.3.3)
#>  classInt      0.4-10  2023-09-05 [1] CRAN (R 4.3.0)
#>  cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  DBI           1.2.2   2024-02-16 [1] CRAN (R 4.3.1)
#>  digest        0.6.35  2024-03-11 [1] CRAN (R 4.3.1)
#>  dplyr       * 1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
#>  e1071         1.7-14  2023-12-06 [1] CRAN (R 4.3.1)
#>  evaluate      0.23    2023-11-01 [1] CRAN (R 4.3.1)
#>  fansi         1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  generics      0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue          1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
#>  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
#>  KernSmooth    2.23-22 2023-07-10 [2] CRAN (R 4.3.3)
#>  knitr         1.45    2023-10-30 [1] CRAN (R 4.3.1)
#>  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr      2.0.3   2022-03-30 [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)
#>  proxy         0.4-27  2022-06-09 [1] CRAN (R 4.3.0)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache       0.16.0  2022-07-21 [2] CRAN (R 4.3.0)
#>  R.methodsS3   1.8.2   2022-06-13 [2] CRAN (R 4.3.0)
#>  R.oo          1.26.0  2024-01-24 [2] CRAN (R 4.3.1)
#>  R.utils       2.12.3  2023-11-18 [2] CRAN (R 4.3.1)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  Rcpp          1.0.12  2024-01-09 [1] CRAN (R 4.3.1)
#>  reprex        2.1.0   2024-01-11 [2] CRAN (R 4.3.1)
#>  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
#>  rmarkdown     2.26    2024-03-05 [1] CRAN (R 4.3.1)
#>  rstudioapi    0.16.0  2024-03-24 [1] CRAN (R 4.3.1)
#>  sessioninfo   1.2.2   2021-12-06 [2] CRAN (R 4.3.0)
#>  sf          * 1.0-16  2024-03-24 [1] CRAN (R 4.3.1)
#>  styler        1.10.3  2024-04-07 [2] CRAN (R 4.3.1)
#>  tibble      * 3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect    1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
#>  units         0.8-5   2023-11-28 [1] CRAN (R 4.3.1)
#>  utf8          1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  winch         0.1.1   2024-02-19 [1] CRAN (R 4.3.1)
#>  withr         3.0.0   2024-01-16 [1] CRAN (R 4.3.1)
#>  xfun          0.43    2024-03-25 [1] CRAN (R 4.3.1)
#>  yaml          2.3.8   2023-12-11 [1] CRAN (R 4.3.1)
#> 
#>  [1] /Users/nick/Library/R/arm64/4.3/library
#>  [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

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4 participants
@bart1 @njtierney @DanChaltiel @avsdev-cw