Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>

mauro_lepore · April 8, 2020, 11:05pm

With the development version of vctrs and a data frame with subclass "spec_tbl_df", tidyr::pivot_longer() throws

#> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>

The error goes away by either attaching readr or removing the class "spec_tbl_df".

Does this look like an issue worth reporting? Which package should it be submitted?

packageVersion("vctrs")
#> [1] '0.2.99.9011'
packageVersion("tidyr")
#> [1] '1.0.2'
packageVersion("readr")
#> [1] '1.3.1'

# install.packages(r2dii.data)
(data <- dplyr::select(r2dii.data::loanbook_demo, 1:2)[1, ])
#> # A tibble: 1 x 2
#>   id_loan id_direct_loantaker
#>   <chr>   <chr>              
#> 1 L1      C294

class(data)
#> [1] "spec_tbl_df" "tbl_df"      "tbl"         "data.frame"
# Fails
tidyr::pivot_longer(data, cols = 1:2)
#> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>.

class(data[])
#> [1] "spec_tbl_df" "tbl_df"      "tbl"         "data.frame"
# Fails
tidyr::pivot_longer(data[], cols = 1:2)
#> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>.

# Create a copy to solve show two solutions
data1 <- data



# It works if I strip the class "spec_tbl_df"
# Solution 1: Explicitely
class(data) <- c("tbl_df", "tbl", "data.frame")
tidyr::pivot_longer(data, cols = 1:2)
#> # A tibble: 2 x 2
#>   name                value
#>   <chr>               <chr>
#> 1 id_loan             L1   
#> 2 id_direct_loantaker C294

# Solution 1: Via readr
library(readr)
tidyr::pivot_longer(data1, cols = 1:2)
#> # A tibble: 2 x 2
#>   name                value
#>   <chr>               <chr>
#> 1 id_loan             L1   
#> 2 id_direct_loantaker C294

^{Created on 2020-04-08 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
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#> 
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#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

mara · April 10, 2020, 2:35pm

Was just about to respond here when the GH issue came through:

github.com/tidyverse/tidyr

With vctrs-dev: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>

opened 02:21PM - 10 Apr 20 UTC

closed 02:37PM - 10 Apr 20 UTC

maurolepore

With the development version of vctrs and a specific a data frame with subclass …"spec_tbl_df", `tidyr::pivot_longer()` throws ``` #> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>> ``` * There is no error with the released version of vctrs. * The error goes away by either attaching readr or removing the class "spec_tbl_df". ``` r packageVersion("vctrs") #> [1] '0.2.99.9011' packageVersion("tidyr") #> [1] '1.0.2' packageVersion("readr") #> [1] '1.3.1' # install.packages(r2dii.data) # Sorry I failed to build a reprex with a generic dataset that exposes the problem (data <- dplyr::select(r2dii.data::loanbook_demo, 1:2)[1, ]) #> # A tibble: 1 x 2 #> id_loan id_direct_loantaker #> <chr> <chr> #> 1 L1 C294 class(data) #> [1] "spec_tbl_df" "tbl_df" "tbl" "data.frame" # Fails tidyr::pivot_longer(data, cols = 1:2) #> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>. class(data[]) #> [1] "spec_tbl_df" "tbl_df" "tbl" "data.frame" # Fails tidyr::pivot_longer(data[], cols = 1:2) #> Error: Can't combine `..1` <spec_tbl_df<>> and `..2` <tbl_df<>>. # Create a copy to solve show two solutions data1 <- data # It works if I strip the class "spec_tbl_df" # Solution 1: Explicitely class(data) <- c("tbl_df", "tbl", "data.frame") tidyr::pivot_longer(data, cols = 1:2) #> # A tibble: 2 x 2 #> name value #> <chr> <chr> #> 1 id_loan L1 #> 2 id_direct_loantaker C294 # Solution 1: Via readr library(readr) tidyr::pivot_longer(data1, cols = 1:2) #> # A tibble: 2 x 2 #> name value #> <chr> <chr> #> 1 id_loan L1 #> 2 id_direct_loantaker C294 ``` Created on 2020-04-08 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) <details> <summary>Session info</summary> ``` r devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 3.6.3 (2020-02-29) #> os Ubuntu 18.04.4 LTS #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/Chicago #> date 2020-04-08 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.6 2020-04-05 [1] #> callr 3.4.3 2020-03-28 [1] #> cli 2.0.2 2020-02-28 [1] #> crayon 1.3.4.9000 2020-04-08 [1] #> desc 1.2.0 2018-05-01 [1] #> devtools 2.2.2 2020-02-17 [1] #> digest 0.6.25 2020-02-23 [1] #> dplyr 0.8.5 2020-03-07 [1] #> ellipsis 0.3.0 2019-09-20 [1] #> evaluate 0.14 2019-05-28 [1] #> fansi 0.4.1 2020-01-08 [1] #> fs 1.4.1 2020-04-04 [1] #> glue 1.4.0 2020-04-03 [1] #> highr 0.8 2019-03-20 [1] #> hms 0.5.3 2020-01-08 [1] #> htmltools 0.4.0 2019-10-04 [1] #> knitr 1.28 2020-02-06 [1] #> lifecycle 0.2.0 2020-03-06 [1] #> magrittr 1.5 2014-11-22 [1] #> memoise 1.1.0 2017-04-21 [1] #> pillar 1.4.3 2019-12-20 [1] #> pkgbuild 1.0.6 2019-10-09 [1] #> pkgconfig 2.0.3 2019-09-22 [1] #> pkgload 1.0.2 2018-10-29 [1] #> prettyunits 1.1.1 2020-01-24 [1] #> processx 3.4.2 2020-02-09 [1] #> ps 1.3.2 2020-02-13 [1] #> purrr 0.3.3 2019-10-18 [1] #> r2dii.data 0.0.3.9000 2020-04-06 [1] #> R6 2.4.1 2019-11-12 [1] #> Rcpp 1.0.4 2020-03-17 [1] #> readr * 1.3.1 2018-12-21 [1] #> remotes 2.1.1 2020-02-15 [1] #> rlang 0.4.5.9000 2020-03-22 [1] #> rmarkdown 2.1 2020-01-20 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> stringi 1.4.6 2020-02-17 [1] #> stringr 1.4.0 2019-02-10 [1] #> testthat 2.3.2 2020-03-02 [1] #> tibble 3.0.0 2020-03-30 [1] #> tidyr 1.0.2 2020-01-24 [1] #> tidyselect 1.0.0 2020-01-27 [1] #> usethis 1.5.1.9000 2020-03-22 [1] #> utf8 1.1.4 2018-05-24 [1] #> vctrs 0.2.99.9011 2020-04-08 [1] #> withr 2.1.2 2018-03-15 [1] #> xfun 0.12 2020-01-13 [1] #> yaml 2.2.1 2020-02-01 [1] #> source #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> Github (r-lib/crayon@e949005) #> CRAN (R 3.6.3) #> standard (@2.2.2) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@0.14) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@0.8) #> CRAN (R 3.6.3) #> standard (@0.4.0) #> standard (@1.28) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@1.1.0) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@1.0.2) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@0.3.3) #> Github (2degreesinvesting/r2dii.data@321e703) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@1.3.1) #> standard (@2.1.1) #> Github (r-lib/rlang@a90b04b) #> standard (@2.1) #> CRAN (R 3.6.3) #> standard (@1.1.1) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> standard (@2.3.2) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> CRAN (R 3.6.3) #> Github (r-lib/usethis@6f62e04) #> CRAN (R 3.6.3) #> Github (r-lib/vctrs@2d7ce56) #> CRAN (R 3.6.3) #> standard (@0.12) #> standard (@2.2.1) #> #> [1] /home/mauro/R/x86_64-pc-linux-gnu-library/3.6 #> [2] /usr/local/lib/R/site-library #> [3] /usr/lib/R/site-library #> [4] /usr/lib/R/library ``` </details>

The issue is being tracked in vctrs here:

github.com/r-lib/vctrs

Problems with dplyr bind_row() and tidyr pivot_longer() in combination with vctrs after upgrade.

opened 04:53PM - 08 Apr 20 UTC

closed 05:56PM - 24 Apr 20 UTC

BenPVD

bug type:dataframe

Hi, I was tempted and did the upgrade to the development version of `dplyr` a…fter reading a bit in the blog post from @Hadley released earlier this week. Unfortunately, this broke my existing script at two locations, once (so far I have to say) at a `dplyr::bind_rows` position and once at a `tidyr::pivot_longer` position. During the upgrade of `dplyr` to the development version, `vctrs` was updated as well. I will not post my whole script here, since this would be too much, so I stored my environment prior to the error and just run the function creating the error in the code section below. I did not change anything on the script itself! The only things I changed between the executions are the versions of either `dplyr` or `vctrs` and a downgrade (installation from CRAN) of `dplyr` and `vctrs` restored my script. ``` r load(file = "~/troubleshoot.RData") DT_count_tab = dplyr::bind_rows(DT_count_tab, .id = "sample_id") #> Error: Can't convert <data.table< #> percentage_reads : double #> total_number_reads : integer #> Vsegm : character #> Jsegm : character #> frame_info : character #> frame_shift : integer #> ORF_info : character #> aa1_peptide_seq_insert: character #> aa2_peptide_seq_total : character #> aa2_dna_seq : character #> >> to <data.table< #> sample_id : character #> percentage_reads : double #> total_number_reads : integer #> Vsegm : character #> Jsegm : character #> frame_info : character #> frame_shift : integer #> ORF_info : character #> aa1_peptide_seq_insert: character #> aa2_peptide_seq_total : character #> aa2_dna_seq : character #> >>. sessionInfo() #> R version 3.6.0 (2019-04-26) #> Platform: x86_64-redhat-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] Rcpp_1.0.4 knitr_1.28 magrittr_1.5 tidyselect_1.0.0 #> [5] R6_2.4.1 rlang_0.4.5.9000 fansi_0.4.1 stringr_1.4.0 #> [9] highr_0.8 dplyr_0.8.99.9002 tools_3.6.0 xfun_0.12 #> [13] cli_2.0.2 htmltools_0.4.0 ellipsis_0.3.0 yaml_2.2.1 #> [17] digest_0.6.25 assertthat_0.2.1 tibble_3.0.0 lifecycle_0.2.0 #> [21] crayon_1.3.4 purrr_0.3.3 vctrs_0.2.99.9011 glue_1.4.0 #> [25] evaluate_0.14 rmarkdown_2.1 stringi_1.4.6 compiler_3.6.0 #> [29] pillar_1.4.3 generics_0.0.2 pkgconfig_2.0.3 ``` Created on 2020-04-08 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) A downgrade of `dplyr` alone (**not** `vctrs`) resolved the issue with the `dplyr::bind_rows()` function, as seen below. ``` r load(file = "~/troubleshoot.RData") DT_count_tab = dplyr::bind_rows(DT_count_tab, .id = "sample_id") sessionInfo() #> R version 3.6.0 (2019-04-26) #> Platform: x86_64-redhat-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] Rcpp_1.0.4 knitr_1.28 magrittr_1.5 tidyselect_1.0.0 #> [5] R6_2.4.1 rlang_0.4.5.9000 fansi_0.4.1 stringr_1.4.0 #> [9] highr_0.8 dplyr_0.8.5 tools_3.6.0 xfun_0.12 #> [13] cli_2.0.2 htmltools_0.4.0 ellipsis_0.3.0 yaml_2.2.1 #> [17] assertthat_0.2.1 digest_0.6.25 tibble_3.0.0 lifecycle_0.2.0 #> [21] crayon_1.3.4 purrr_0.3.3 vctrs_0.2.99.9011 glue_1.4.0 #> [25] evaluate_0.14 rmarkdown_2.1 stringi_1.4.6 compiler_3.6.0 #> [29] pillar_1.4.3 pkgconfig_2.0.3 ``` Created on 2020-04-08 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) The `tidyr::pivot_longer()` was of course not resolved by downgrading `dplyr`. Here, a downgrade of `vctrs` resolved the issue, as shown using both `reprex` outputs below. The first output uses `vctrs` version 0.2.99.9011 and results in an error, the other one was executed after a downgrade of `vctrs` and did not produce any errors. ``` r load(file = "~/troubleshoot.RData") 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(tidyr) new_obj = tmp_DT_count_tab_summary %>% dplyr::select(patient_id, sample_type, study_week, min_clone_count, max_clone_count) %>% tidyr::pivot_longer(data = ., cols = c("min_clone_count", "max_clone_count"), names_to = "range", values_to = "count") #> Error: Can't combine `..1` <data.table<>> and `..2` <tbl_df<>>. sessionInfo() #> R version 3.6.0 (2019-04-26) #> Platform: x86_64-redhat-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] tidyr_1.0.2.9000 dplyr_0.8.5 #> #> loaded via a namespace (and not attached): #> [1] Rcpp_1.0.4 knitr_1.28 magrittr_1.5 tidyselect_1.0.0 #> [5] R6_2.4.1 rlang_0.4.5.9000 fansi_0.4.1 stringr_1.4.0 #> [9] highr_0.8 tools_3.6.0 xfun_0.12 cli_2.0.2 #> [13] htmltools_0.4.0 ellipsis_0.3.0 yaml_2.2.1 assertthat_0.2.1 #> [17] digest_0.6.25 tibble_3.0.0 lifecycle_0.2.0 crayon_1.3.4 #> [21] purrr_0.3.3 vctrs_0.2.99.9011 glue_1.4.0 evaluate_0.14 #> [25] rmarkdown_2.1 stringi_1.4.6 compiler_3.6.0 pillar_1.4.3 #> [29] pkgconfig_2.0.3 ``` Created on 2020-04-08 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) Traceback for this error is: ``` > traceback() 25: stop(fallback) 24: signal_abort(cnd) 23: abort(message, class = c(class, "vctrs_error"), ...) 22: stop_vctrs(message, class = c(class, "vctrs_error_incompatible"), x = x, y = y, details = details, ...) 21: stop_incompatible(x, y, x_arg = x_arg, y_arg = y_arg, details = details, ..., message = message, class = c(class, "vctrs_error_incompatible_type")) 20: stop_incompatible_type_impl(x = x, y = y, x_arg = x_arg, y_arg = y_arg, details = details, action = "combine", ..., message = message, class = class) 19: stop_incompatible_type_combine(x = x, y = y, x_arg = x_arg, y_arg = y_arg, details = details, ..., message = message, class = class) 18: stop_incompatible_type(x, y, x_arg = x_arg, y_arg = y_arg) 17: vec_default_ptype2(x = x, y = y, x_arg = x_arg, y_arg = y_arg) 16: vec_cbind(vec_slice(df_out, rows$df_id), vec_slice(keys, rows$key_id), vec_slice(vals, rows$val_id), .name_repair = names_repair) 15: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(code, vctrs_error_names = function(cnd) { abort(c("Failed to create output due to bad names.", "Choose another strategy with `names_repair`"), parent = cnd) }) 11: wrap_error_names(vec_cbind(vec_slice(df_out, rows$df_id), vec_slice(keys, rows$key_id), vec_slice(vals, rows$val_id), .name_repair = names_repair)) 10: pivot_longer_spec(data, spec, names_repair = names_repair, values_drop_na = values_drop_na, values_ptypes = values_ptypes) 9: tidyr::pivot_longer(data = ., cols = c("min_clone_count", "max_clone_count"), names_to = "range", values_to = "count") 8: function_list[[k]](value) 7: withVisible(function_list[[k]](value)) 6: freduce(value, `_function_list`) 5: `_fseq`(`_lhs`) 4: eval(quote(`_fseq`(`_lhs`)), env, env) 3: eval(quote(`_fseq`(`_lhs`)), env, env) 2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env)) 1: tmp_DT_count_tab_summary %>% dplyr::select(patient_id, sample_type, study_week, min_clone_count, max_clone_count) %>% tidyr::pivot_longer(data = ., cols = c("min_clone_count", "max_clone_count"), names_to = "range", values_to = "count") ``` Code which executes just fine with `vctrs` version 0.2.4: ``` r load(file = "~/troubleshoot.RData") 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(tidyr) new_obj = tmp_DT_count_tab_summary %>% dplyr::select(patient_id, sample_type, study_week, min_clone_count, max_clone_count) %>% tidyr::pivot_longer(data = ., cols = c("min_clone_count", "max_clone_count"), names_to = "range", values_to = "count") sessionInfo() #> R version 3.6.0 (2019-04-26) #> Platform: x86_64-redhat-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C #> [9] LC_ADDRESS=C LC_TELEPHONE=C #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] tidyr_1.0.2.9000 dplyr_0.8.5 #> #> loaded via a namespace (and not attached): #> [1] Rcpp_1.0.4 knitr_1.28 magrittr_1.5 tidyselect_1.0.0 #> [5] R6_2.4.1 rlang_0.4.5.9000 fansi_0.4.1 stringr_1.4.0 #> [9] highr_0.8 tools_3.6.0 xfun_0.12 cli_2.0.2 #> [13] htmltools_0.4.0 ellipsis_0.3.0 yaml_2.2.1 assertthat_0.2.1 #> [17] digest_0.6.25 tibble_3.0.0 lifecycle_0.2.0 crayon_1.3.4 #> [21] purrr_0.3.3 vctrs_0.2.4 glue_1.4.0 evaluate_0.14 #> [25] rmarkdown_2.1 stringi_1.4.6 compiler_3.6.0 pillar_1.4.3 #> [29] pkgconfig_2.0.3 ``` Created on 2020-04-08 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) I hope all this is clearly explained. I know this might not be the best way of a submission of an issue today, but I wanted to put this out in case it is not reported yet (I saw some discussion about `vctrs` and row binding...) Thanks much for the support!

system · May 1, 2020, 2:35pm

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