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RQGIS3 chrashed my RStudio session #10

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Robinlovelace opened this issue May 30, 2019 · 11 comments
Open

RQGIS3 chrashed my RStudio session #10

Robinlovelace opened this issue May 30, 2019 · 11 comments

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@Robinlovelace
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Reporting as it has happened twice and seems to be reproducible. I followed the README on 18.04 with the following results:

image
@Robinlovelace
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Session info below. Thinking it may be an issue with my setup. Regardless, QGIS3 should never cause RStudio to crash (could also be an RStudio issue):

rstudioapi::versionInfo()
#> Error: RStudio not running
system("apt list --installed | grep ^qgis", intern = TRUE)
#> [1] "qgis/bionic,now 1:3.4.8+28bionic-ubuntugis amd64 [installed]"                                   
#> [2] "qgis-common/bionic,bionic,now 1:3.4.8+28bionic-ubuntugis all [installed,automatic]"             
#> [3] "qgis-plugin-grass/bionic,now 1:3.4.8+28bionic-ubuntugis amd64 [installed]"                      
#> [4] "qgis-plugin-grass-common/bionic,bionic,now 1:3.4.8+28bionic-ubuntugis all [installed,automatic]"
#> [5] "qgis-provider-grass/bionic,now 1:3.4.8+28bionic-ubuntugis amd64 [installed,automatic]"          
#> [6] "qgis-providers/bionic,now 1:3.4.8+28bionic-ubuntugis amd64 [installed,automatic]"               
#> [7] "qgis-providers-common/bionic,bionic,now 1:3.4.8+28bionic-ubuntugis all [installed,automatic]"
system("apt list --installed | grep ^grass", intern = TRUE)
#> [1] "grass/bionic,bionic,now 7.6.1-1~bionic1 all [installed]"              
#> [2] "grass-core/bionic,now 7.6.1-1~bionic1 amd64 [installed,automatic]"    
#> [3] "grass-doc/bionic,bionic,now 7.6.1-1~bionic1 all [installed,automatic]"
#> [4] "grass-gui/bionic,now 7.6.1-1~bionic1 amd64 [installed,automatic]"
system("apt list --installed | grep ^python3.6", intern = TRUE)
#> [1] "python3.6/bionic-updates,now 3.6.7-1~18.04 amd64 [installed]"              
#> [2] "python3.6-dev/bionic-updates,now 3.6.7-1~18.04 amd64 [installed,automatic]"
#> [3] "python3.6-minimal/bionic-updates,now 3.6.7-1~18.04 amd64 [installed]"
library(RQGIS3)
#> Loading required package: reticulate
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       Ubuntu 18.04.2 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/London               
#>  date     2019-05-30                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                          
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                  
#>  backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                  
#>  callr         3.2.0      2019-03-15 [1] standard (@3.2.0)               
#>  class         7.3-15     2019-01-01 [1] standard (@7.3-15)              
#>  classInt      0.3-3      2019-04-26 [1] CRAN (R 3.6.0)                  
#>  cli           1.1.0      2019-03-19 [1] CRAN (R 3.5.3)                  
#>  codetools     0.2-16     2018-12-24 [3] CRAN (R 3.5.2)                  
#>  crayon        1.3.4      2017-09-16 [1] standard (@1.3.4)               
#>  DBI           1.0.0      2018-05-02 [1] CRAN (R 3.5.2)                  
#>  desc          1.2.0      2018-05-01 [1] standard (@1.2.0)               
#>  devtools      2.0.2      2019-04-08 [1] CRAN (R 3.6.0)                  
#>  digest        0.6.19     2019-05-20 [2] CRAN (R 3.6.0)                  
#>  e1071         1.7-1      2019-03-19 [1] CRAN (R 3.5.3)                  
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                  
#>  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                  
#>  glue          1.3.1      2019-03-12 [1] CRAN (R 3.5.3)                  
#>  highr         0.8        2019-03-20 [2] CRAN (R 3.5.3)                  
#>  hms           0.4.2      2018-03-10 [1] CRAN (R 3.5.3)                  
#>  htmltools     0.3.6      2017-04-28 [2] CRAN (R 3.5.0)                  
#>  jsonlite      1.6        2018-12-07 [1] standard (@1.6)                 
#>  KernSmooth    2.23-15    2015-06-29 [3] CRAN (R 3.5.0)                  
#>  knitr         1.23       2019-05-18 [2] CRAN (R 3.6.0)                  
#>  lattice       0.20-38    2018-11-04 [1] standard (@0.20-38)             
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 3.5.2)                  
#>  Matrix        1.2-17     2019-03-22 [1] CRAN (R 3.6.0)                  
#>  memoise       1.1.0      2017-04-21 [2] CRAN (R 3.5.0)                  
#>  pillar        1.4.1      2019-05-28 [1] CRAN (R 3.6.0)                  
#>  pkgbuild      1.0.3      2019-03-20 [1] standard (@1.0.3)               
#>  pkgconfig     2.0.2      2018-08-16 [1] standard (@2.0.2)               
#>  pkgload       1.0.2      2018-10-29 [2] CRAN (R 3.5.1)                  
#>  prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.5.3)                  
#>  processx      3.3.1      2019-05-08 [1] CRAN (R 3.6.0)                  
#>  ps            1.3.0      2018-12-21 [1] CRAN (R 3.5.3)                  
#>  R6            2.4.0      2019-02-14 [1] standard (@2.4.0)               
#>  raster        2.9-5      2019-05-14 [1] CRAN (R 3.6.0)                  
#>  Rcpp          1.0.1      2019-03-17 [1] CRAN (R 3.5.3)                  
#>  readr         1.3.1      2018-12-21 [1] CRAN (R 3.5.3)                  
#>  remotes       2.0.4      2019-04-10 [1] CRAN (R 3.6.0)                  
#>  reticulate  * 1.12       2019-04-12 [1] CRAN (R 3.6.0)                  
#>  rgdal         1.4-4      2019-05-29 [1] CRAN (R 3.6.0)                  
#>  rlang         0.3.4      2019-04-07 [1] CRAN (R 3.6.0)                  
#>  rmarkdown     1.13       2019-05-22 [2] CRAN (R 3.6.0)                  
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.5.3)                  
#>  RQGIS3      * 1.0.1.9000 2019-05-30 [1] Github (jannes-m/RQGIS3@35e9faa)
#>  rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.5.3)                  
#>  sessioninfo   1.1.1      2018-11-05 [2] CRAN (R 3.5.1)                  
#>  sf            0.7-4      2019-04-25 [1] CRAN (R 3.6.0)                  
#>  sp            1.3-1      2018-06-05 [1] CRAN (R 3.5.3)                  
#>  stringi       1.4.3      2019-03-12 [1] CRAN (R 3.5.3)                  
#>  stringr       1.4.0      2019-02-10 [1] standard (@1.4.0)               
#>  testthat      2.1.1      2019-04-23 [1] CRAN (R 3.6.0)                  
#>  tibble        2.1.2      2019-05-29 [1] CRAN (R 3.6.0)                  
#>  units         0.6-3      2019-05-03 [1] CRAN (R 3.6.0)                  
#>  usethis       1.5.0      2019-04-07 [2] CRAN (R 3.5.3)                  
#>  withr         2.1.2      2018-03-15 [1] CRAN (R 3.5.3)                  
#>  xfun          0.7        2019-05-14 [2] CRAN (R 3.6.0)                  
#>  yaml          2.2.0      2018-07-25 [2] CRAN (R 3.5.1)                  
#> 
#> [1] /usr/local/lib/R/site-library
#> [2] /usr/lib/R/site-library
#> [3] /usr/lib/R/library

Created on 2019-05-30 by the reprex package (v0.3.0)

@Robinlovelace
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I'm on RStudio 1.2.1326 btw,

@Robinlovelace
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Also crashed on the latest version of RStudio, just installed.

@Robinlovelace
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Amazingly, it runs fine when not in RStudio. I seem to recall this issue in previous conversations with @jannes-m:

library(RQGIS3)
#> Loading required package: reticulate
    set_env()
#> Assuming that your root path is '/usr'!
#> $root
#> [1] "/usr"
#> 
#> $qgis_prefix_path
#> [1] "/usr/bin/qgis"
#> 
#> $python_plugins
#> [1] "/usr/share/qgis/python/plugins"
    find_algorithms("centroid")
#> [1] "Centroids-------------------------------------------->native:centroids"                               
#> [2] "Generate points (pixel centroids) along line--------->qgis:generatepointspixelcentroidsalongline"     
#> [3] "Generate points (pixel centroids) inside polygons---->qgis:generatepointspixelcentroidsinsidepolygons"
#> [4] "Polygon centroids------------------------------------>saga:polygoncentroids"

Created on 2019-05-30 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       Ubuntu 18.04.2 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/London               
#>  date     2019-05-30                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                          
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                  
#>  backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                  
#>  callr         3.2.0      2019-03-15 [1] standard (@3.2.0)               
#>  class         7.3-15     2019-01-01 [1] standard (@7.3-15)              
#>  classInt      0.3-3      2019-04-26 [1] CRAN (R 3.6.0)                  
#>  cli           1.1.0      2019-03-19 [1] CRAN (R 3.5.3)                  
#>  codetools     0.2-16     2018-12-24 [3] CRAN (R 3.5.2)                  
#>  crayon        1.3.4      2017-09-16 [1] standard (@1.3.4)               
#>  DBI           1.0.0      2018-05-02 [1] CRAN (R 3.5.2)                  
#>  desc          1.2.0      2018-05-01 [1] standard (@1.2.0)               
#>  devtools      2.0.2      2019-04-08 [1] CRAN (R 3.6.0)                  
#>  digest        0.6.19     2019-05-20 [2] CRAN (R 3.6.0)                  
#>  e1071         1.7-1      2019-03-19 [1] CRAN (R 3.5.3)                  
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                  
#>  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                  
#>  glue          1.3.1      2019-03-12 [1] CRAN (R 3.5.3)                  
#>  highr         0.8        2019-03-20 [2] CRAN (R 3.5.3)                  
#>  hms           0.4.2      2018-03-10 [1] CRAN (R 3.5.3)                  
#>  htmltools     0.3.6      2017-04-28 [2] CRAN (R 3.5.0)                  
#>  jsonlite      1.6        2018-12-07 [1] standard (@1.6)                 
#>  KernSmooth    2.23-15    2015-06-29 [3] CRAN (R 3.5.0)                  
#>  knitr         1.23       2019-05-18 [2] CRAN (R 3.6.0)                  
#>  lattice       0.20-38    2018-11-04 [1] standard (@0.20-38)             
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 3.5.2)                  
#>  Matrix        1.2-17     2019-03-22 [1] CRAN (R 3.6.0)                  
#>  memoise       1.1.0      2017-04-21 [2] CRAN (R 3.5.0)                  
#>  pillar        1.4.1      2019-05-28 [1] CRAN (R 3.6.0)                  
#>  pkgbuild      1.0.3      2019-03-20 [1] standard (@1.0.3)               
#>  pkgconfig     2.0.2      2018-08-16 [1] standard (@2.0.2)               
#>  pkgload       1.0.2      2018-10-29 [2] CRAN (R 3.5.1)                  
#>  prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.5.3)                  
#>  processx      3.3.1      2019-05-08 [1] CRAN (R 3.6.0)                  
#>  ps            1.3.0      2018-12-21 [1] CRAN (R 3.5.3)                  
#>  R6            2.4.0      2019-02-14 [1] standard (@2.4.0)               
#>  raster        2.9-5      2019-05-14 [1] CRAN (R 3.6.0)                  
#>  Rcpp          1.0.1      2019-03-17 [1] CRAN (R 3.5.3)                  
#>  readr         1.3.1      2018-12-21 [1] CRAN (R 3.5.3)                  
#>  remotes       2.0.4      2019-04-10 [1] CRAN (R 3.6.0)                  
#>  reticulate  * 1.12       2019-04-12 [1] CRAN (R 3.6.0)                  
#>  rgdal         1.4-4      2019-05-29 [1] CRAN (R 3.6.0)                  
#>  rlang         0.3.4      2019-04-07 [1] CRAN (R 3.6.0)                  
#>  rmarkdown     1.13       2019-05-22 [2] CRAN (R 3.6.0)                  
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.5.3)                  
#>  RQGIS3      * 1.0.1.9000 2019-05-30 [1] Github (jannes-m/RQGIS3@35e9faa)
#>  sessioninfo   1.1.1      2018-11-05 [2] CRAN (R 3.5.1)                  
#>  sf            0.7-4      2019-04-25 [1] CRAN (R 3.6.0)                  
#>  sp            1.3-1      2018-06-05 [1] CRAN (R 3.5.3)                  
#>  stringi       1.4.3      2019-03-12 [1] CRAN (R 3.5.3)                  
#>  stringr       1.4.0      2019-02-10 [1] standard (@1.4.0)               
#>  testthat      2.1.1      2019-04-23 [1] CRAN (R 3.6.0)                  
#>  tibble        2.1.2      2019-05-29 [1] CRAN (R 3.6.0)                  
#>  units         0.6-3      2019-05-03 [1] CRAN (R 3.6.0)                  
#>  usethis       1.5.0      2019-04-07 [2] CRAN (R 3.5.3)                  
#>  withr         2.1.2      2018-03-15 [1] CRAN (R 3.5.3)                  
#>  xfun          0.7        2019-05-14 [2] CRAN (R 3.6.0)                  
#>  yaml          2.2.0      2018-07-25 [2] CRAN (R 3.5.1)                  
#> 
#> [1] /usr/local/lib/R/site-library
#> [2] /usr/lib/R/site-library
#> [3] /usr/lib/R/library

@Robinlovelace
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Another example, from a terminal this time:

library(RQGIS3)
Loading required package: reticulate
> set_env()
Assuming that your root path is '/usr'!
$root
[1] "/usr"

$qgis_prefix_path
[1] "/usr/bin/qgis"

$python_plugins
[1] "/usr/share/qgis/python/plugins"

> find_algorithms("clean")
/usr/share/qgis/python/plugins/processing/algs/help/__init__.py:46: YAMLLoadWarning:

calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.

/usr/share/qgis/python/plugins/processing/algs/help/__init__.py:46: YAMLLoadWarning:

calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.

/usr/share/qgis/python/plugins/processing/gui/wrappers.py:1757: DeprecationWarning:

invalid escape sequence \A

/usr/share/qgis/python/plugins/processing/gui/wrappers.py:1772: DeprecationWarning:

invalid escape sequence \A

[1] "v.clean---------------------------------------------->grass7:v.clean"
>

@Robinlovelace Robinlovelace mentioned this issue May 30, 2019
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@mwip
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mwip commented Nov 27, 2019

I can reproduce this behavior. Also running on Ubuntu 18.04-LTS.

@Robinlovelace
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It seems hard to debug. @jannes-m am I right in thinking that your recommended work-around is to use our docker image? I recall we added QGIS to a version of the Dockerfile, the main one IIRC.

@jannes-m
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Yes, RQGIS3 and Rstudio work in harmony in the geocompr Docker image and under Windows. Another way would be to use R from the cli.

@vaibhavgupta13
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Hello @jannes-m, I did not want to create a new issue for this because it is probably very straightforward but I am unable to move forward. I could find help anywhere else hence asking the question here so sorry for the hassle.
My issue is that I am unable to install RQGIS3 on my machine. First it asked me to install Rtools which I did and then I tried a number of ways to try and install RQGIS3 but it says that the plugin doesn't exist.
I don't remember facing this issue whilst installing/working with RQGIS (older plugin). For reference, I am using a Windows 10 64 bit machine. Any help would be greatly appreciated. Thanks

@Robinlovelace
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Can you install Docker? That is an alternative way to get it working.

@vaibhavgupta13
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Thanks @Robinlovelace , I managed to somehow get it to install. Let's see if I'm able to get it to work finally. :)

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@Robinlovelace @jannes-m @vaibhavgupta13 @mwip