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Solve prints out annoying text about `tbl_df` #75

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jeffreyhanson opened this Issue Apr 24, 2018 · 14 comments

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jeffreyhanson commented Apr 24, 2018

The solve function prints out the following text when it is run. It should not do this.

## Found more than one class "tbl_df" in cache; using the first, from namespace 'prioritizr'

@jeffreyhanson jeffreyhanson added the bug label Apr 24, 2018

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jeffreyhanson commented Apr 24, 2018

This can be reproduced using the following code in a fresh R session.

# load packaege
library(prioritizr)

# simulate data
costs <- raster::raster(matrix(c(1, 2, NA, 3), ncol = 4))
spp <- raster::stack(raster::raster(matrix(c(1, 2, 0, 0), ncol = 4)),
                     raster::raster(matrix(c(NA, 0, 1, 1), ncol = 4)))
# make problem
p <- problem(costs, spp) %>%
     add_min_set_objective() %>%
     add_absolute_targets(c(1, 1)) %>%
     add_binary_decisions() %>%
     add_rsymphony_solver(gap = 0, verbose = FALSE)

# solve problem
solve(p)
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javierfajnolla commented Jul 19, 2018

Hi!

I am still experiencing this issue very often. It happens not only for the solve() function, but also related to functions related to the tibble package (like, as_tibble(), tibble()..., which are used internally quite often if you use dplyr). I think that this happens to me since I upgraded to prioritizr v4, but I am not sure.

Are you sure the patch for avoiding the repeated warning is properly working?

I am experiencing this on a mac, using Rstudio and R version 3.5.1, prioritizr_4.0.2.1 and tibble_1.4.2.

Thanks for the help!
Javier

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jeffreyhanson commented Jul 19, 2018

Hey, yeah, I thought I fixed this back in April but yeah it seems to have come back. I'll reopen this issue and see what I can do.

@jeffreyhanson jeffreyhanson reopened this Jul 19, 2018

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jeffreyhanson commented Jul 21, 2018

@javierfajnolla, can you please post a short reproducible example showing this behaviour? I'm trying to come up with a short example but I'm having trouble.

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javierfajnolla commented Jul 21, 2018

Sure!
But... it actually happens to me all the time at so many actions that do not involve prioritizr. Look at this simple lines:

Restarting R session...

> library(tidyverse)
── Attaching packages ───────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
> library(prioritizr)
Loading required package: raster
Loading required package: sp

Attaching package: ‘raster’

The following object is masked from ‘package:dplyr’:

    select

The following object is masked from ‘package:tidyr’:

    extract

Loading required package: proto
> example <- tibble(
+   col1 = c(1:3),
+   col2 = c(4:6)
+ )
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] prioritizr_4.0.2.1 proto_1.0.0        raster_2.6-7      
 [4] sp_1.3-1           forcats_0.3.0      stringr_1.3.1     
 [7] dplyr_0.7.6        purrr_0.2.5        readr_1.1.1       
[10] tidyr_0.8.1        tibble_1.4.2       ggplot2_3.0.0     
[13] tidyverse_1.2.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17     cellranger_1.1.0 pillar_1.3.0     compiler_3.5.1  
 [5] plyr_1.8.4       bindr_0.1.1      tools_3.5.1      jsonlite_1.5    
 [9] lubridate_1.7.4  nlme_3.1-137     gtable_0.2.0     lattice_0.20-35 
[13] pkgconfig_2.0.1  rlang_0.2.1      Matrix_1.2-14    cli_1.0.0       
[17] rstudioapi_0.7   yaml_2.1.19      haven_1.1.2      bindrcpp_0.2.2  
[21] withr_2.1.2      xml2_1.2.0       httr_1.3.1       hms_0.4.2       
[25] grid_3.5.1       tidyselect_0.2.4 glue_1.2.0       R6_2.2.2        
[29] readxl_1.1.0     modelr_0.1.2     magrittr_1.5     backports_1.1.2 
[33] scales_0.5.0     rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2
[37] stringi_1.2.3    lazyeval_0.2.1   munsell_0.5.0    broom_0.5.0     
[41] crayon_1.3.4

Just using tibble() shows the warning, which is printed several times.
Are you thinking in another type of example of that one helps you?

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jeffreyhanson commented Jul 21, 2018

Thanks for the quick response! Yeah, I can't seem to reproduce this on my machine (see below for session info). I just ran that code you posted in R 3.5.1 on Ubuntu 16.04 and it doesn't print the cache stuff. I'll post an issue in the tibble repo on GitHub, would you mind if I @'d you in the issue and if they try to implement a fix, could you please verify if it works?


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /opt/R/R-3.5.1/lib/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.1/lib/R/lib/libRlapack.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] prioritizr_4.0.2 proto_1.0.0      raster_2.6-7     sp_1.3-1        
 [5] forcats_0.3.0    stringr_1.3.1    dplyr_0.7.5      purrr_0.2.5     
 [9] readr_1.1.1      tidyr_0.8.1      tibble_1.4.2     ggplot2_2.2.1   
[13] tidyverse_1.2.1 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17     cellranger_1.1.0 pillar_1.2.3     compiler_3.5.1  
 [5] plyr_1.8.4       bindr_0.1.1      tools_3.5.1      jsonlite_1.5    
 [9] lubridate_1.7.4  gtable_0.2.0     nlme_3.1-137     lattice_0.20-35 
[13] pkgconfig_2.0.1  rlang_0.2.1      Matrix_1.2-14    cli_1.0.0       
[17] rstudioapi_0.7   haven_1.1.2      bindrcpp_0.2.2   xml2_1.2.0      
[21] httr_1.3.1       hms_0.4.2        grid_3.5.1       tidyselect_0.2.4
[25] glue_1.2.0       R6_2.2.2         readxl_1.1.0     modelr_0.1.2    
[29] magrittr_1.5     backports_1.1.2  scales_0.5.0     rvest_0.3.2     
[33] assertthat_0.2.0 colorspace_1.3-2 utf8_1.1.4       stringi_1.2.3   
[37] lazyeval_0.2.1   munsell_0.5.0    broom_0.5.0      crayon_1.3.4 
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javierfajnolla commented Jul 21, 2018

Sure! Happy to help, you can @'d me.

Interestingly, I find the same issue at a windows machine I have access to (with slightly different package versions installed). Look at the output there I just got for the same code:

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Workspace loaded from ~/.RData]

Loading required package: raster
Loading required package: sp

Restarting R session...

> library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.2     v dplyr   0.7.4
v tidyr   0.8.0     v stringr 1.3.0
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
> library(prioritizr)
Loading required package: raster
Loading required package: sp

Attaching package: ‘raster’

The following object is masked from ‘package:dplyr’:

    select

The following object is masked from ‘package:tidyr’:

    extract

Loading required package: proto
> example <- tibble(
+   col1 = c(1:3),
+   col2 = c(4:6)
+ )
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Chile.1252  LC_CTYPE=Spanish_Chile.1252   
[3] LC_MONETARY=Spanish_Chile.1252 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Chile.1252    

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

other attached packages:
 [1] prioritizr_4.0.2.1 proto_1.0.0        raster_2.6-7       sp_1.3-1          
 [5] forcats_0.3.0      stringr_1.3.0      dplyr_0.7.4        purrr_0.2.4       
 [9] readr_1.1.1        tidyr_0.8.0        tibble_1.4.2       ggplot2_2.2.1     
[13] tidyverse_1.2.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17     cellranger_1.1.0 pillar_1.2.1     compiler_3.4.4   plyr_1.8.4      
 [6] bindr_0.1.1      tools_3.4.4      lubridate_1.7.3  jsonlite_1.5     nlme_3.1-131.1  
[11] gtable_0.2.0     lattice_0.20-35  pkgconfig_2.0.1  rlang_0.2.0      Matrix_1.2-12   
[16] psych_1.8.3.3    cli_1.0.0        rstudioapi_0.7   yaml_2.1.18      parallel_3.4.4  
[21] haven_1.1.1      bindrcpp_0.2.2   xml2_1.2.0       httr_1.3.1       hms_0.4.2       
[26] grid_3.4.4       glue_1.2.0       R6_2.2.2         readxl_1.0.0     foreign_0.8-69  
[31] modelr_0.1.1     reshape2_1.4.3   magrittr_1.5     scales_0.5.0     rvest_0.3.2     
[36] assertthat_0.2.0 mnormt_1.5-5     colorspace_1.3-2 stringi_1.1.7    lazyeval_0.2.1  
[41] munsell_0.4.3    broom_0.4.4      crayon_1.3.4  
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jeffreyhanson commented Jul 21, 2018

Awesome - thanks - I'll post the issue now.

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jeffreyhanson commented Jul 23, 2018

As per tidyverse/tibble#434, @javierfajnolla, I've created a modified version of the tibble package (jeffreyhanson/tibble) and an experimental version of prioritizr in a new branch (prioritizr/prioritizr@tibbles4) to see if we can fix the problem. Could you please install these packages and try running your code and see if you still encounter the problem? You can install the packages with the following code:

devtools::install_github("jeffreyhanson/tibble")
devtools::install_github("prioritizr/prioritizr@tibbles4")
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javierfajnolla commented Jul 23, 2018

Hi Jeff!

Thanks for the effort in solving this.
So, it seems that the changes you made do the trick. I do not get the warning anymore:

I installed them in dev_mode

devtools::dev_mode(on = T)
devtools::install_github("jeffreyhanson/tibble")
devtools::install_github("prioritizr/prioritizr@tibbles4")

After installing:

d> library(tibble)
d> library(prioritizr)
Loading required package: raster
Loading required package: sp
Loading required package: proto
d> example <- tibble(
+   col1 = c(1:3),
+   col2 = c(4:6)
+ )
d> example
# A tibble: 3 x 2
   col1  col2
  <int> <int>
1     1     4
2     2     5
3     3     6
d> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] prioritizr_4.0.2.3 proto_1.0.0        raster_2.6-7      
[4] sp_1.3-1           tibble_1.4.2.9004 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      rstudioapi_0.7    knitr_1.20       
 [4] magrittr_1.5      devtools_1.13.6   lattice_0.20-35  
 [7] R6_2.2.2          rlang_0.2.1       fansi_0.2.3      
[10] httr_1.3.1        tools_3.5.1       grid_3.5.1       
[13] utf8_1.1.4        cli_1.0.0         git2r_0.22.1     
[16] withr_2.1.2       assertthat_0.2.0  yaml_2.1.19      
[19] digest_0.6.15     crayon_1.3.4      Matrix_1.2-14    
[22] curl_3.2          memoise_1.1.0     compiler_3.5.1   
[25] pillar_1.3.0.9000

As you can see, no warnings!

I double checked that dev_mode was using the new versions of the packages by restarting R and reproducing the warning with the old version of the packages.

Thanks a lot again!
Best regards,
Javier

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jeffreyhanson commented Jul 24, 2018

Ok great - thank you - I haven't tried dev mode in devtools before it sounds very useful. Before I submit a PR to tibble, could you please verify that you still get the cache stuff printed out when you use the CRAN versions of prioritizr and tibble in dev mode? I've found that sometimes having a package loaded using functions (i.e. devtools::load_all()) can give slightly different experiences then when loading them normally.

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javierfajnolla commented Jul 24, 2018

Oh, yes!
The warnings are there if I use the CRAN version of the packages in dev_mode. So, it seems to me that the fixes work...
(I am not so used to dev_mode either, shouldn't have taken the risk).

This is the complete output for both versions of the packages (first CRAN, later your prepared forks), everything inside dev_mode:

> devtools::dev_mode(on = T)
Dev mode: ON
d> # devtools::install_github("jeffreyhanson/tibble")
d> # devtools::install_github("prioritizr/prioritizr@tibbles4")
d> install.packages("tibble")
Installing package into ‘/Users/javierfajnolla/R-dev’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/tibble_1.4.2.tgz'
Content type 'application/x-gzip' length 230077 bytes (224 KB)
==================================================
downloaded 224 KB


The downloaded binary packages are in
	/var/folders/n3/w4wvn5k50rx9nm4mdk6v8dvw0000gn/T//RtmpI0AagA/downloaded_packages
d> install.packages("prioritizr")
Installing package into ‘/Users/javierfajnolla/R-dev’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/prioritizr_4.0.2.tgz'
Content type 'application/x-gzip' length 2094124 bytes (2.0 MB)
==================================================
downloaded 2.0 MB


The downloaded binary packages are in
	/var/folders/n3/w4wvn5k50rx9nm4mdk6v8dvw0000gn/T//RtmpI0AagA/downloaded_packages
d> library(tibble)
d> library(prioritizr)
Loading required package: raster
Loading required package: sp
Loading required package: proto
d> example <- tibble(
+   col1 = c(1:3),
+   col2 = c(4:6)
+ )
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'
Also defined by ‘prioritizr’
d> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] prioritizr_4.0.2 proto_1.0.0      raster_2.6-7     sp_1.3-1        
[5] tibble_1.4.2    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      lattice_0.20-35   digest_0.6.15    
 [4] crayon_1.3.4      withr_2.1.2       grid_3.5.1       
 [7] magrittr_1.5      pillar_1.3.0.9000 rlang_0.2.1      
[10] rstudioapi_0.7    Matrix_1.2-14     devtools_1.13.6  
[13] tools_3.5.1       yaml_2.1.19       compiler_3.5.1   
[16] memoise_1.1.0    
d> devtools::dev_mode(on = F)
Dev mode: OFF

Restarting R session...

> devtools::dev_mode(on = T)
Dev mode: ON
d> devtools::install_github("jeffreyhanson/tibble")
  (...)
d> devtools::install_github("prioritizr/prioritizr@tibbles4")
  (...)

(there I omitted the long installation console output)

* DONE (prioritizr)
d> 
d> library(tibble)
d> library(prioritizr)
Loading required package: raster
Loading required package: sp
Loading required package: proto
d> 
d> example <- tibble(
+   col1 = c(1:3),
+   col2 = c(4:6)
+ )
d> example
# A tibble: 3 x 2
   col1  col2
  <int> <int>
1     1     4
2     2     5
3     3     6
d> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] prioritizr_4.0.2.3 proto_1.0.0        raster_2.6-7      
[4] sp_1.3-1           tibble_1.4.2.9004 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      rstudioapi_0.7    knitr_1.20       
 [4] magrittr_1.5      devtools_1.13.6   lattice_0.20-35  
 [7] R6_2.2.2          rlang_0.2.1       fansi_0.2.3      
[10] httr_1.3.1        tools_3.5.1       grid_3.5.1       
[13] utf8_1.1.4        cli_1.0.0         git2r_0.22.1     
[16] withr_2.1.2       assertthat_0.2.0  yaml_2.1.19      
[19] digest_0.6.15     crayon_1.3.4      Matrix_1.2-14    
[22] curl_3.2          memoise_1.1.0     compiler_3.5.1   
[25] pillar_1.3.0.9000

Does it look as expected to you?
Thanks for helping so much!
Javier

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jeffreyhanson commented Jul 24, 2018

Yeah - perfect - thank you very much! I'll submit the PR now.

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jeffreyhanson commented Jul 31, 2018

They've just merged the PR so now the developmental version of tibble on GitHub is updated so that we can modify prioritizr so that it doesn't print all the annoying text. Unfortunately, we can't actually update the CRAN version of prioritizr to stop printing the annoying text until they update the version of tibble on CRAN with the fix. So, I'll just keep this issue open for the moment and keep an eye out for when they update the version of tibble on CRAN.

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