RQGIS3 chrashed my RStudio session
Robinlovelace opened this issue · 11 comments
Robinlovelace commented
Reporting as it has happened twice and seems to be reproducible. I followed the README on 18.04 with the following results:
Robinlovelace commented
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/libraryCreated on 2019-05-30 by the reprex package (v0.3.0)
Robinlovelace commented
I'm on RStudio 1.2.1326 btw,
Robinlovelace commented
Also crashed on the latest version of RStudio, just installed.
Robinlovelace commented
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/libraryRobinlovelace commented
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"
>
mwip commented
I can reproduce this behavior. Also running on Ubuntu 18.04-LTS.
Robinlovelace commented
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 commented
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 commented
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 commented
Can you install Docker? That is an alternative way to get it working.
vaibhavgupta13 commented
Thanks @Robinlovelace , I managed to somehow get it to install. Let's see if I'm able to get it to work finally. :)