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collateral not on cran anymore? #18

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MatthieuStigler opened this issue May 23, 2020 · 7 comments
Closed

collateral not on cran anymore? #18

MatthieuStigler opened this issue May 23, 2020 · 7 comments

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@MatthieuStigler
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Hi

I just noticed collateral is not on cran anymore. I am also facing issues using has_errors, such as: rror: Input must be a vector, not a safely_mapped object. Are these issues linked? Maybe the latter is linked to the developments in the vctrs package? What is the status anyway of the package?

Thanks!

@jimjam-slam
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Hi Matthieu,

I'm afraid I've been a little slow getting the next Collateral release up on CRAN. I've received advice about the issue you're seeing (it's linked to the tibble 1.0 and dplyr 1.0 releases) but should have a simple fix that I'm hoping to test and submit to CRAN this week. I'm sorry for the disruption!

@jimjam-slam
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Update: I've made these fixes and pushed them to dev. Everything seems to be working for me, and my checks are all passing! However, I won't be able to submit this version (0.5.1) to CRAN until I can uodate to R 4.0.0 and test on that.

@MatthieuStigler
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I tried with the dev version, and still am getting the error message. I would not be surorised if it came from updates in vctrs ?

library(tidyverse)
library(collateral)
sessionInfo()
#> R version 4.0.0 (2020-04-24)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04 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=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] collateral_0.5.0.9001 forcats_0.5.0         stringr_1.4.0        
#>  [4] dplyr_0.8.5           purrr_0.3.4           readr_1.3.1          
#>  [7] tidyr_1.0.3           tibble_3.0.1          ggplot2_3.3.0        
#> [10] tidyverse_1.3.0      
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_1.1.0 xfun_0.13        haven_2.2.0      lattice_0.20-41 
#>  [5] colorspace_1.4-1 vctrs_0.3.0      generics_0.0.2   htmltools_0.4.0 
#>  [9] yaml_2.2.1       rlang_0.4.6      pillar_1.4.4     glue_1.4.1      
#> [13] withr_2.2.0      DBI_1.1.0        dbplyr_1.4.3     modelr_0.1.7    
#> [17] readxl_1.3.1     lifecycle_0.2.0  munsell_0.5.0    gtable_0.3.0    
#> [21] cellranger_1.1.0 rvest_0.3.5      evaluate_0.14    knitr_1.28      
#> [25] fansi_0.4.1      highr_0.8        broom_0.5.6      Rcpp_1.0.4.6    
#> [29] scales_1.1.1     backports_1.1.7  jsonlite_1.6.1   fs_1.4.1        
#> [33] hms_0.5.3        digest_0.6.25    stringi_1.4.6    grid_4.0.0      
#> [37] cli_2.0.2        tools_4.0.0      magrittr_1.5     crayon_1.3.4    
#> [41] pkgconfig_2.0.3  ellipsis_0.3.1   xml2_1.3.2       reprex_0.3.0    
#> [45] lubridate_1.7.8  assertthat_0.2.1 rmarkdown_2.1    httr_1.4.1      
#> [49] R6_2.4.1         nlme_3.1-147     compiler_4.0.0
packageVersion("collateral")
#> [1] '0.5.0.9001'

iris %>% 
  nest(data=-Species) %>% 
  mutate(mean=map_safely(data, ~mean(.$Petal.Length))) %>% 
  filter(has_errors(mean))
#> Error: Input must be a vector, not a `safely_mapped` object.

Created on 2020-05-26 by the reprex package (v0.3.0)

@jimjam-slam
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jimjam-slam commented Jul 20, 2020

@MatthieuStigler I haven't been able to replicate this with my packages updated, but I am getting other warnings crop up:

> iris %>% nest(data = -Species)
# # A tibble: 3 x 2
#   Species    data             
#   <fct>      <list>           
# 1 setosa     <tibble [50 x 4]>
# 2 versicolor <tibble [50 x 4]>
# 3 virginica  <tibble [50 x 4]>
# Warning message:
# `...` is not empty.
# 
# We detected these problematic arguments:
# * `needs_dots`
# 
# These dots only exist to allow future extensions and should be empty.
# Did you misspecify an argument? 

@jimjam-slam
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Update: ah, this appears to be a problem in tibble that is fixed in 3.0.3. I'm able to run your code without error now:

> iris %>% 
+     nest(data=-Species) %>% 
+     mutate(mean=map_safely(data, ~mean(.$Petal.Length)))
# A tibble: 3 x 3
  Species    data              mean    
  <fct>      <list>            <collat>
1 setosa     <tibble [50 x 4]> R _     
2 versicolor <tibble [50 x 4]> R _     
3 virginica  <tibble [50 x 4]> R _     
> iris %>% 
+     nest(data=-Species) %>% 
+     mutate(mean=map_safely(data, ~mean(.$Petal.Length))) %>% 
+     filter(has_errors(mean))
# A tibble: 0 x 3
# ... with 3 variables: Species <fct>, data <list>, mean <collat>

I've attached my session info below 😊 This will likely be my CRAN release candidate, as I'm keen to fill the void following my tardiness! My session info below—I'm not sure that we've quite isolated this between the updates to tibble, dplyr, tidyr, pillar and vctrs, but I get the impression there've been a few teething bug-point releases following this major upgrade cycle.

- Session info --------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.0 (2020-04-24)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United Kingdom.1252 
 ctype    English_United Kingdom.1252 
 tz       Australia/Sydney            
 date     2020-07-20                  

- Packages ------------------------------------------------------------------------------------------------
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
 backports     1.1.6   2020-04-05 [1] CRAN (R 4.0.0)
 broom         0.5.6   2020-04-20 [1] CRAN (R 4.0.0)
 callr         3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
 cellranger    1.1.0   2016-07-27 [1] CRAN (R 4.0.0)
 cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
 codetools     0.2-16  2018-12-24 [2] CRAN (R 4.0.0)
 collateral  * 0.5.1   2020-07-20 [1] local         
 colorspace    1.4-1   2019-03-18 [1] CRAN (R 4.0.0)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
 DBI           1.1.0   2019-12-15 [1] CRAN (R 4.0.0)
 dbplyr        1.4.3   2020-04-19 [1] CRAN (R 4.0.0)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
 devtools      2.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
 dplyr       * 0.8.5   2020-03-07 [1] CRAN (R 4.0.0)
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.0)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
 forcats     * 0.5.0   2020-03-01 [1] CRAN (R 4.0.0)
 fs            1.4.1   2020-04-04 [1] CRAN (R 4.0.0)
 furrr         0.1.0   2018-05-16 [1] CRAN (R 4.0.0)
 future        1.17.0  2020-04-18 [1] CRAN (R 4.0.0)
 generics      0.0.2   2018-11-29 [1] CRAN (R 4.0.0)
 ggplot2     * 3.3.0   2020-03-05 [1] CRAN (R 4.0.0)
 globals       0.12.5  2019-12-07 [1] CRAN (R 4.0.0)
 glue          1.4.1   2020-05-13 [1] CRAN (R 4.0.0)
 gtable        0.3.0   2019-03-25 [1] CRAN (R 4.0.0)
 haven         2.2.0   2019-11-08 [1] CRAN (R 4.0.0)
 hms           0.5.3   2020-01-08 [1] CRAN (R 4.0.0)
 httr          1.4.1   2019-08-05 [1] CRAN (R 4.0.0)
 jsonlite      1.6.1   2020-02-02 [1] CRAN (R 4.0.0)
 lattice       0.20-41 2020-04-02 [2] CRAN (R 4.0.0)
 lifecycle     0.2.0   2020-03-06 [1] CRAN (R 4.0.0)
 listenv       0.8.0   2019-12-05 [1] CRAN (R 4.0.0)
 lubridate     1.7.8   2020-04-06 [1] CRAN (R 4.0.0)
 magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
 modelr        0.1.8   2020-05-19 [1] CRAN (R 4.0.0)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 4.0.0)
 nlme          3.1-147 2020-04-13 [2] CRAN (R 4.0.0)
 pillar        1.4.6   2020-07-10 [1] CRAN (R 4.0.2)
 pkgbuild      1.0.8   2020-05-07 [1] CRAN (R 4.0.0)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.0)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 4.0.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
 processx      3.4.2   2020-02-09 [1] CRAN (R 4.0.0)
 ps            1.3.3   2020-05-08 [1] CRAN (R 4.0.0)
 purrr       * 0.3.4   2020-04-17 [1] CRAN (R 4.0.0)
 R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 Rcpp          1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
 readr       * 1.3.1   2018-12-21 [1] CRAN (R 4.0.0)
 readxl        1.3.1   2019-03-13 [1] CRAN (R 4.0.0)
 remotes       2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
 reprex        0.3.0   2019-05-16 [1] CRAN (R 4.0.0)
 rlang         0.4.7   2020-07-09 [1] CRAN (R 4.0.2)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
 rstudioapi    0.11    2020-02-07 [1] CRAN (R 4.0.0)
 rvest         0.3.5   2019-11-08 [1] CRAN (R 4.0.0)
 scales        1.1.1   2020-05-11 [1] CRAN (R 4.0.0)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
 stringi       1.4.6   2020-02-17 [1] CRAN (R 4.0.0)
 stringr     * 1.4.0   2019-02-10 [1] CRAN (R 4.0.0)
 testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
 tibble      * 3.0.3   2020-07-10 [1] CRAN (R 4.0.2)
 tidyr       * 1.1.0   2020-05-20 [1] CRAN (R 4.0.0)
 tidyselect    1.1.0   2020-05-11 [1] CRAN (R 4.0.0)
 tidyverse   * 1.3.0   2019-11-21 [1] CRAN (R 4.0.0)
 usethis       1.6.1   2020-04-29 [1] CRAN (R 4.0.0)
 utf8          1.1.4   2018-05-24 [1] CRAN (R 4.0.0)
 vctrs         0.3.2   2020-07-15 [1] CRAN (R 4.0.2)
 withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.0)
 xml2          1.3.2   2020-04-23 [1] CRAN (R 4.0.0)

@MatthieuStigler
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Thanks for checking James!!

Indeed, after updating all packages, and once getting the current version of collateral, I don't have the problem anymore, youhou!!

Thanks!

@jimjam-slam
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Phew! I'll get this sent off to CRAN ASAP 😁

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