Failed installation without clear error message

[yoelii]

I try to install "tidyverse" R package with pak.

The function run but never finish :

> library("pak")
> pkg_install("tidyverse")
v Updated metadata database: 4.35 MB in 9 files.                          
v Updating metadata database ... done   

My R sessionInfo()

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so 
LAPACK: /usr/local/lib/R/lib/libRlapack.so;  LAPACK version 3.12.0
locale:
[1] C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] pak_0.7.2     ggplot2_3.5.1
loaded via a namespace (and not attached):
 [1] utf8_1.2.4       R6_2.5.1         tidyselect_1.2.1 magrittr_2.0.3  
 [5] gtable_0.3.5     glue_1.7.0       tibble_3.2.1     pkgconfig_2.0.3 
 [9] generics_0.1.3   dplyr_1.1.4      lifecycle_1.0.4  cli_3.6.3       
[13] fansi_1.0.6      scales_1.3.0     grid_4.4.0       vctrs_0.6.5     
[17] withr_3.0.0      compiler_4.4.0   tools_4.4.0      munsell_0.5.1   
[21] pillar_1.9.0     colorspace_2.1-0 rlang_1.1.4     

If I kill my R Session and I try again, the function failed early, still without error message :

> library("pak")
> pkg_install("tidyverse")
v Loading metadata database ... done

Same failed issue with :

> pkg_sysreqs("tidyverse")
v Loading metadata database ... done

I suppose a system dependency is missing or trouble with rights maybes but I have no error message, only look like run correctly but never finish

Thank for your help

[gaborcsardi]

Can you include the actual error messages?

Also, what is the output of this?

getOption("repos")

[yoelii]

I have no message. The function still running infinite. I need to kill my R session.

> getOption("repos")
[1] "https://cran.r-project.org"

[yoelii]

I try to install with install.packages("tidyverse") and it's work well, after I install some system dependencies ( apt-get install -y libfribidi-dev libharfbuzz-dev )

But pkg_intall("tidyverse") still failed.

If I remove the package, and try agin a installation with pak, it run with success

remove.packages("tidyverse")
Removing package from '/usr/local/lib/R/library'
(as 'lib' is unspecified)
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> pkg_install("tidyverse")
v Loading metadata database ... done                                                                        
> Will install 1 package.
> Will download 1 package with unknown size.
+ tidyverse   2.0.0 [bld][dl]
v All system requirements are already installed.
i Getting 1 pkg with unknown size
v Got tidyverse 2.0.0 (source) (704.62 kB)                               
v Downloaded 1 package (704.62 kB) in 685ms                              
i Building tidyverse 2.0.0
v Built tidyverse 2.0.0 (1.3s)                                                
v Installed tidyverse 2.0.0  (26ms)                                             
v 1 pkg + 102 deps: kept 91, added 1, dld 1 (704.62 kB) [5.7s]  

I don't understand why

[gaborcsardi]

Set your repository like this:

options(repos = c(CRAN = "cran.R-project.org"))

I would also suggest to use https://packagemanager.posit.co/client/#/, so you don't need to compile packages from source:

options(repos = c(
  P3M = "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
  CRAN = "https://cloud.r-project.org"
))

[yoelii]

Thanks,

it work after set the repository and without install the system dependency :

options(repos = c(CRAN = "cran.R-project.org"))

> library("pak")
> options(repos = c(CRAN = "cran.R-project.org"))
> pkg_install("tidyverse")
v Updated metadata database: 2.95 MB in 7 files.                          
v Updating metadata database ... done                                     
                                                                            
> Will install 39 packages.
> Will download 39 CRAN packages (14.53 MB).
+ DBI             1.2.3  [bld][dl] (1.13 MB)
+ backports       1.5.0  [bld][cmp][dl] (26.20 kB)
+ bit             4.0.5  [bld][cmp][dl] (827.75 kB)
+ bit64           4.0.5  [bld][cmp][dl] (135.09 kB)
+ blob            1.2.4  [bld][dl] (10.62 kB)
+ broom           1.0.6  [bld][dl] (641.85 kB)
+ cellranger      1.1.0  [bld][dl] (63.86 kB)
+ clipr           0.8.0  [bld][dl] (21.90 kB)
+ conflicted      1.2.0  [bld][dl] (17.07 kB)
+ dbplyr          2.5.0  [bld][dl] (770.65 kB)
+ dtplyr          1.3.1  [bld][dl] (150.97 kB)
+ forcats         1.0.0  [bld][dl] (294.18 kB)
+ gargle          1.5.2  [bld][dl] (627.56 kB)
+ googledrive     2.1.1  [bld][dl] (1.61 MB)
+ googlesheets4   1.1.1  [bld][dl] (232.58 kB)
+ haven           2.5.4  [bld][cmp][dl] (313.33 kB) + v make, v zlib1g-dev
+ hms             1.1.3  [bld][dl] (43.38 kB)
+ ids             1.0.1  [bld][dl] (91.21 kB)
+ lubridate       1.9.3  [bld][cmp][dl] (428.04 kB)
+ modelr          0.1.11 [bld][dl] (121.48 kB)
+ prettyunits     1.2.0  [bld][dl] (97.50 kB)
+ progress        1.2.3  [bld][dl] (30.50 kB)
+ ragg            1.3.2  [bld][cmp][dl] (430.24 kB) + v libfreetype6-dev, v libjpeg-dev, v libpng-dev, v libtiff-dev
+ readr           2.1.5  [bld][cmp][dl] (298.06 kB)
+ readxl          1.4.3  [bld][cmp][dl] (2.09 MB)
+ rematch         2.0.0  [bld][dl] (4.78 kB)
+ rematch2        2.1.2  [bld][dl] (13.37 kB)
+ reprex          2.1.1  [bld][dl] (1.09 MB) + x pandoc
+ rstudioapi      0.16.0 [bld][dl] (117.42 kB)
+ rvest           1.0.4  [bld][dl] (115.88 kB)
+ selectr         0.4-2  [bld][dl] (41.37 kB)
+ systemfonts     1.1.0  [bld][cmp][dl] (80.84 kB) + v libfontconfig1-dev, v libfreetype6-dev
+ textshaping     0.4.0  [bld][cmp][dl] (35.10 kB) + v libfreetype6-dev, x libfribidi-dev, x libharfbuzz-dev
+ tidyverse       2.0.0  [bld][dl] (704.62 kB)
+ timechange      0.3.0  [bld][cmp][dl] (103.44 kB)
+ tzdb            0.4.0  [bld][cmp][dl] (586.33 kB)
+ uuid            1.2-1  [bld][cmp][dl] (79.72 kB)
+ vroom           1.6.5  [bld][cmp][dl] (750.42 kB)
+ xml2            1.3.6  [bld][cmp][dl] (294.71 kB) + v libxml2-dev
> Will install 3 system packages:
+ libfribidi-dev   - textshaping             
+ libharfbuzz-dev  - textshaping             
+ pandoc           - reprex, knitr, rmarkdown
i Getting 39 pkgs (14.53 MB)
v Got backports 1.5.0 (source) (30.69 kB)                                                              
v Got blob 1.2.4 (source) (10.62 kB)                                                                   
v Got bit64 4.0.5 (source) (135.09 kB)                                                                                                              
v Got dtplyr 1.3.1 (source) (150.97 kB)                                                                                                             
v Got haven 2.5.4 (source) (313.33 kB)                                                                                                              
v Got broom 1.0.6 (source) (641.54 kB)                                                                                                                                                         
v Got bit 4.0.5 (source) (827.75 kB)                                                                                                                                                           
v Got gargle 1.5.2 (source) (627.56 kB)                                                                                                                             
v Got readr 2.1.5 (source) (298.06 kB)                                                                                                                              
v Got lubridate 1.9.3 (source) (428.04 kB)                                                                                                                          
v Got rstudioapi 0.16.0 (source) (117.42 kB)                                                                                                                        
v Got rvest 1.0.4 (source) (115.88 kB)                                                                                                                           
v Got systemfonts 1.1.0 (source) (85.58 kB)                                                                                                                      
v Got clipr 0.8.0 (source) (21.90 kB)                                                                                                                            
v Got conflicted 1.2.0 (source) (17.07 kB)                                                                                   
v Got hms 1.1.3 (source) (43.38 kB)                                                                                          
v Got textshaping 0.4.0 (source) (37.96 kB)                                                                                  
v Got tidyverse 2.0.0 (source) (704.62 kB)                                                                                   
v Got tzdb 0.4.0 (source) (586.33 kB)                                                                                                                    
v Got vroom 1.6.5 (source) (750.42 kB)                                                                                                                   
v Got progress 1.2.3 (source) (30.50 kB)                                                                                                                                                  
v Got rematch 2.0.0 (source) (4.78 kB)                                                                                                                                                    
v Got DBI 1.2.3 (source) (1.14 MB)                                                                                                                                                                
v Got googlesheets4 1.1.1 (source) (232.58 kB)                                                                                                                                                    
v Got reprex 2.1.1 (source) (1.09 MB)                                                                                                                                                             
v Got selectr 0.4-2 (source) (41.37 kB)                                                                                                                                                           
v Got cellranger 1.1.0 (source) (63.86 kB)                                                                                                                                                        
v Got timechange 0.3.0 (source) (103.44 kB)                                                                                
v Got prettyunits 1.2.0 (source) (97.50 kB)                                                                                
v Got uuid 1.2-1 (source) (80.66 kB)                                                                                       
v Got modelr 0.1.11 (source) (121.48 kB)                                                                                            
v Got ids 1.0.1 (source) (91.21 kB)                                                                                                 
v Got forcats 1.0.0 (source) (294.18 kB)                                                                                            
v Got xml2 1.3.6 (source) (294.71 kB)                                                                                               
v Got rematch2 2.1.2 (source) (13.37 kB)                                                                              
v Got ragg 1.3.2 (source) (430.37 kB)                                                                                 
v Got readxl 1.4.3 (source) (2.09 MB)                                                                                 
v Got dbplyr 2.5.0 (source) (770.65 kB)                                                         
v Got googledrive 2.1.1 (source) (1.61 MB)                                                      
v Downloaded 39 packages (14.54 MB) in 2.3s                                             
i Installing system requirements
i Executing `sh -c apt-get -y update`
i Executing `sh -c apt-get -y install pandoc libfribidi-dev libharfbuzz-dev`
i Building backports 1.5.0
i Building bit 4.0.5
i Building blob 1.2.4
i Building clipr 0.8.0
i Building conflicted 1.2.0
i Building DBI 1.2.3
i Building dtplyr 1.3.1
i Building forcats 1.0.0
i Building gargle 1.5.2
i Building hms 1.1.3
i Building prettyunits 1.2.0
i Building rematch 2.0.0
i Building rematch2 2.1.2
i Building rstudioapi 0.16.0
i Building selectr 0.4-2
i Building systemfonts 1.1.0
v Built clipr 0.8.0 (1.6s)                                                                                                                                                                                      
i Building timechange 0.3.0                                                                                                                                                                                     
v Built blob 1.2.4 (1.9s)                                                                                                                                                                                            
v Built conflicted 1.2.0 (1.9s)                                                                                                                                                                                      
i Building tzdb 0.4.0                                                                                                                                                                                                
v Built backports 1.5.0 (2.5s)                                                                                                                                                                                 
i Building uuid 1.2-1                                                                                                                                                                                    
v Built rematch 2.0.0 (1.6s)                                                                                                                                                                             
i Building xml2 1.3.6                                                                                                                                                                               
v Installed backports 1.5.0  (74ms)                                                                                                                                                                                    
i Building broom 1.0.6                                                                                                                                                                                                 
v Built hms 1.1.3 (2.8s)                                                                                                                                                                                               
v Built prettyunits 1.2.0 (2.8s)                                                                                                                                                                        
v Installed blob 1.2.4  (52ms)                                                                                                                                                                          
v Installed clipr 0.8.0  (118ms)                                                                                                                                                                                    
v Installed conflicted 1.2.0  (109ms)                                                                                                                                                                               
v Built forcats 1.0.0 (3.8s)                                                                                                                                                                                        
v Built rematch2 2.1.2 (3.3s)                                                                                                                                                                         
v Installed hms 1.1.3  (152ms)                                                                                                                                                                        
v Built rstudioapi 0.16.0 (3.2s)                                                                                                                                                             
v Installed forcats 1.0.0  (152ms)                                                                                                                                                      
v Installed prettyunits 1.2.0  (83ms)                                                                                                                                                   
i Building progress 1.2.3                                                                                                                                                               
v Installed rematch 2.0.0  (38ms)                                                                                                                                                    
i Building cellranger 1.1.0                                                                                                                                                          
v Installed rematch2 2.1.2  (36ms)                                                                                                                                                                
v Installed rstudioapi 0.16.0  (49ms)                                                                                                                                                               
i Building reprex 2.1.1                                                                                                                                                                             
v Built dtplyr 1.3.1 (6.4s)                                                                                                                                                                         
v Installed dtplyr 1.3.1  (53ms)                                                                                                                                                                
v Built cellranger 1.1.0 (2.4s)                                                                                                                                                                 
v Installed cellranger 1.1.0  (47ms)                                                                                                                                                    
v Built DBI 1.2.3 (7.8s)                                                                                                                                                                
v Built progress 1.2.3 (3.3s)                                                                                                                                               
v Installed DBI 1.2.3  (117ms)                                                                                                                                              
v Installed progress 1.2.3  (80ms)                                                                                                                                          
i Building dbplyr 2.5.0                                                                                                                                                     
i Building readxl 1.4.3                                                                                                                                                
v Built reprex 2.1.1 (3.6s)                                                                                                                                       
v Installed reprex 2.1.1  (52ms)                                                                                                                                             
v Built gargle 1.5.2 (8.7s)                                                                                                                                                  
v Installed gargle 1.5.2  (99ms)                                                                                                                                     
v Built bit 4.0.5 (9.9s)                                                                                                                                             
v Built uuid 1.2-1 (7.4s)                                                                                                                                   
v Installed bit 4.0.5  (115ms)                                                                                                                              
v Installed uuid 1.2-1  (86ms)                                                                                                                              
i Building bit64 4.0.5                                                                                                                                      
i Building googledrive 2.1.1                                                                                                                           
i Building ids 1.0.1                                                                                                                                       
v Built ids 1.0.1 (1.8s)                                                                                                                                        
v Installed ids 1.0.1  (33ms)                                                                                                                                              
v Built selectr 0.4-2 (11.8s)                                                                                                                                              
v Installed selectr 0.4-2  (43ms)                                                                                                                                    
v Built broom 1.0.6 (10.6s)                                                                                                                                          
v Installed broom 1.0.6  (120ms)                                                                                                                            
i Building modelr 0.1.11                                                                                                                                    
v Built googledrive 2.1.1 (4.7s)                                                                                                                            
v Installed googledrive 2.1.1  (59ms)                                                                                                                        
i Building googlesheets4 1.1.1                                                                                                                               
v Built xml2 1.3.6 (12.9s)                                                                                                                                   
v Installed xml2 1.3.6  (51ms)                                                                                                                                 
i Building rvest 1.0.4                                                                                                                                         
v Built modelr 0.1.11 (2.7s)                                                                                                                                   
v Installed modelr 0.1.11  (42ms)                                                                                                                               
v Built bit64 4.0.5 (8.9s)                                                                                                                                      
v Built rvest 1.0.4 (3.3s)                                                                                                                              
v Installed bit64 4.0.5  (96ms)                                                                                                                         
v Installed rvest 1.0.4  (120ms)                                                                                                                        
v Built googlesheets4 1.1.1 (4.3s)                                                                                                               
v Installed googlesheets4 1.1.1  (33ms)                                                                                                   
v Built tzdb 0.4.0 (18.4s)                                                                                                                
v Installed tzdb 0.4.0  (54ms)                                                                                             
i Building vroom 1.6.5                                                                                                     
v Built dbplyr 2.5.0 (14.6s)                                                                                               
v Installed dbplyr 2.5.0  (39ms)                                                                                            
v Built timechange 0.3.0 (23.2s)                                                                                            
v Installed timechange 0.3.0  (64ms)                                                                                
i Building lubridate 1.9.3                                                                                          
v Built readxl 1.4.3 (19.6s)                                                                                        
v Installed readxl 1.4.3  (70ms)                                                                                   
v Built systemfonts 1.1.0 (29.1s)                                                                                  
v Installed systemfonts 1.1.0  (66ms)                                                                      
i Building textshaping 0.4.0                                                                               
v Built lubridate 1.9.3 (5.7s)                                                                             
v Installed lubridate 1.9.3  (32ms)                                                                         
v Built textshaping 0.4.0 (9.4s)                                                                            
v Installed textshaping 0.4.0  (39ms)                                                             
i Building ragg 1.3.2                                                                             
v Built vroom 1.6.5 (59.8s)                                                                       
v Installed vroom 1.6.5  (140ms)                                                           
i Building readr 2.1.5                                                                     
v Built readr 2.1.5 (28s)                                                                  
v Installed readr 2.1.5  (113ms)                                                           
i Building haven 2.5.4                                                                     
v Built haven 2.5.4 (13.6s)                                                                
v Installed haven 2.5.4  (47ms)                                                            
v Built ragg 1.3.2 (1m 46.1s)                                                              
v Installed ragg 1.3.2  (190ms)                                            
i Building tidyverse 2.0.0                                                 
v Built tidyverse 2.0.0 (1.4s)                                                
v Installed tidyverse 2.0.0  (31ms)                                             
v 1 pkg + 105 deps: kept 56, added 39, dld 39 (14.54 MB) [2m 45.3s]   

[gaborcsardi]

AFAICT this is solved now, but please reopen if you have problems. Thanks!