ee_Initialize() crashes Rstudio but works fine through the command line

[DavidDHofmann]

• rgee version:
• R version:
• Operating System:

At submit an issue, please attached the following information of your rgee session:

• [X] You have the Python API installed (from terminal):

  earthengine -h

• [X] You can find the credentials file on your system:

  library(rgee)
  ee_path <- path.expand("~/.config/earthengine/credentials")
  file.exists(ee_path)

• [X] You can run a simple EE command from R:

library(rgee)

# Initialize the Earth Engine module.
ee_Initialize()

# Print metadata for a DEM dataset.
print(ee$Image('USGS/SRTMGL1_003')$getInfo())

Attach your Python (reticulate) configuration:

library(reticulate)
py_config()

Description

Hi there. I'm experiencing some trouble when running rgee in RStudio. When running the function ee_Initialize(), my RStudio session crashes with a "Session Aborted" error. However, the same function works perfectly fine when initiated through the command line. I tried to reinstall RStudio but this didn't solve the issue. Without any error message, I am a bit lost on the potential causes of this behavior.

What I Did

library(rgee)
library(reticulate)
py_config()

python:         /home/david/miniconda3/envs/rgee/bin/python
libpython:      /home/david/miniconda3/envs/rgee/lib/libpython3.6m.so
pythonhome:     /home/david/miniconda3/envs/rgee:/home/david/miniconda3/envs/rgee
version:        3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
numpy:          /home/david/miniconda3/envs/rgee/lib/python3.6/site-packages/numpy
numpy_version:  1.17.0
ee:             /home/david/miniconda3/envs/rgee/lib/python3.6/site-packages/ee

python versions found: 
 /usr/bin/python3
 /home/david/miniconda3/bin/python
 /home/david/miniconda3/envs/rgee/bin/python

ee_check()

◉  Python version
✓ [Ok] /home/david/miniconda3/envs/rgee/bin/python v3.6
◉  Python packages:
✓ [Ok] numpy
✓ [Ok] earthengine-api

ee_Initialize()

-> Session aborts

Here's my sessionInfo

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.3

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=de_CH.UTF-8       LC_NUMERIC=C               LC_TIME=de_CH.UTF-8       
 [4] LC_COLLATE=de_CH.UTF-8     LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=de_CH.UTF-8   
 [7] LC_PAPER=de_CH.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] reticulate_1.23 rgee_1.1.2     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        here_1.0.1        lattice_0.20-45   png_0.1-7         ps_1.6.0         
 [6] rprojroot_2.0.2   digest_0.6.29     crayon_1.4.2      rappdirs_0.3.3    grid_4.1.2       
[11] R6_2.5.1          jsonlite_1.7.2    magrittr_2.0.1    rlang_0.4.12      cli_3.1.0        
[16] rstudioapi_0.13   leaflet_2.0.4.1   Matrix_1.4-0      tools_4.1.2       htmlwidgets_1.5.4
[21] crosstalk_1.2.0   fastmap_1.1.0     compiler_4.1.2    processx_3.5.2    htmltools_0.5.2

[csaybar]

hi @DavidDHofmann can you run.

library(rgee)
ee$Initialize()

• Does the problem continue?
• What version of Rstudio are you using?

[csaybar]

Please create a report and share it with us:

rstudioDiagnosticsReport()
# Diagnostics report written to:  /home/csaybar/rstudio-diagnostics/diagnostics-report.txt

Please audit the report and remove any sensitive information before sharing it!!

[DavidDHofmann]

Hi there and thanks for looking into this.

I tried running ee$Initialize() with the same result, the session simply crashes. Attached you can find the diagnostic report.

RStudio Diagnostics Report
==========================

WARNING: This report may contain sensitive security information and / or
personally identifiable information. Please audit the below and redact any
sensitive information before submitting your diagnostics report.

Generated: Thu Jan 20 09:35:33 2022

RStudio Version
--------------------------------------------------
2021.09.2+382

Session Information
--------------------------------------------------
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.3

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=de_CH.UTF-8       LC_NUMERIC=C               LC_TIME=de_CH.UTF-8       
 [4] LC_COLLATE=de_CH.UTF-8     LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=de_CH.UTF-8   
 [7] LC_PAPER=de_CH.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2   

System Information
--------------------------------------------------
sysname        : Linux                                               
release        : 5.4.0-96-generic                                    
version        : #109~18.04.1-Ubuntu SMP Thu Jan 13 15:06:26 UTC 2022
nodename       : minty                                               
machine        : x86_64                                              
login          : unknown                                             
user           : david                                               
effective_user : david                                               

Platform Information
--------------------------------------------------
OS.type    : unix
file.sep   : /
dynlib.ext : .so
GUI        : RStudio
endian     : little
pkgType    : source
path.sep   : :
r_arch     : 

Environment Variables
--------------------------------------------------
_R_CHECK_COMPILATION_FLAGS_KNOWN_ : -Wformat -Werror=format-security -Wdate-time
CINNAMON_VERSION                  : 4.4.8
CLICOLOR_FORCE                    : 1
DBUS_SESSION_BUS_ADDRESS          : unix:path=/run/user/1000/bus
DEFAULTS_PATH                     : /usr/share/gconf/cinnamon.default.path
DESKTOP_SESSION                   : cinnamon
DISPLAY                           : :0
EARTHENGINE_ENV                   : rgee
EARTHENGINE_INIT_MESSAGE          : True
EARTHENGINE_PYTHON                : /home/david/miniconda3/envs/rgee/bin/python
EDITOR                            : vi
force_s3tc_enable                 : true
GDM_LANG                          : de_CH
GDMSESSION                        : cinnamon
GIO_LAUNCHED_DESKTOP_FILE         : /usr/share/applications/rstudio.desktop
GIO_LAUNCHED_DESKTOP_FILE_PID     : 28343
GIT_ASKPASS                       : rpostback-askpass
GJS_DEBUG_OUTPUT                  : stderr
GJS_DEBUG_TOPICS                  : JS ERROR;JS LOG
GNOME_DESKTOP_SESSION_ID          : this-is-deprecated
GPG_AGENT_INFO                    : /run/user/1000/gnupg/S.gpg-agent:0:1
GTK_MODULES                       : gail:atk-bridge
GTK_OVERLAY_SCROLLING             : 1
HOME                              : /home/david
LANG                              : de_CH.UTF-8
LANGUAGE                          : de_CH:de
LD_LIBRARY_PATH                   : /usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-13-openjdk-amd64/lib/server
LN_S                              : ln -s
LOGNAME                           : *** redacted ***
MAKE                              : make
MANDATORY_PATH                    : /usr/share/gconf/cinnamon.mandatory.path
MPLENGINE                         : tkAgg
PAGER                             : /usr/bin/pager
PATH                              : /home/david/.local/bin:/home/david/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/rstudio/bin/postback
PWD                               : *** redacted ***
PYTHONIOENCODING                  : utf-8
QT_ACCESSIBILITY                  : 1
QT_QPA_PLATFORMTHEME              : qt5ct
R_BROWSER                         : xdg-open
R_BZIPCMD                         : /bin/bzip2
R_DOC_DIR                         : /usr/share/R/doc
R_GZIPCMD                         : /bin/gzip -n
R_HOME                            : /usr/lib/R
R_INCLUDE_DIR                     : /usr/share/R/include
R_LIBS_SITE                       : /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER                       : ~/R/x86_64-pc-linux-gnu-library/4.1
R_PAPERSIZE                       : letter
R_PAPERSIZE_USER                  : a4
R_PDFVIEWER                       : /usr/bin/xdg-open
R_PLATFORM                        : x86_64-pc-linux-gnu
R_PRINTCMD                        : /usr/bin/lpr
R_RD4PDF                          : times,inconsolata,hyper
R_SESSION_TMPDIR                  : /tmp/Rtmp7yFJwI
R_SHARE_DIR                       : /usr/share/R/share
R_STRIP_SHARED_LIB                : strip --strip-unneeded
R_STRIP_STATIC_LIB                : strip --strip-debug
R_SYSTEM_ABI                      : linux,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD                     : /usr/bin/texi2dvi
R_UNZIPCMD                        : /usr/bin/unzip
R_ZIPCMD                          : /usr/bin/zip
RMARKDOWN_MATHJAX_PATH            : /usr/lib/rstudio/resources/mathjax-27
RS_PPM_FD_READ                    : 109
RS_PPM_FD_WRITE                   : 110
RS_RPOSTBACK_PATH                 : /usr/lib/rstudio/bin/rpostback
RS_SHARED_SECRET                  : *** redacted ***
RSTUDIO                           : 1
RSTUDIO_CONSOLE_COLOR             : 256
RSTUDIO_CONSOLE_WIDTH             : 104
RSTUDIO_PANDOC                    : /usr/lib/rstudio/bin/pandoc
RSTUDIO_PROGRAM_MODE              : desktop
RSTUDIO_SESSION_PORT              : 38474
RSTUDIO_USER_IDENTITY             : david
RSTUDIO_WINUTILS                  : bin/winutils
SED                               : /bin/sed
SESSION_MANAGER                   : local/minty:@/tmp/.ICE-unix/2443,unix/minty:/tmp/.ICE-unix/2443
SHELL                             : /bin/bash
SHLVL                             : 0
SSH_AGENT_PID                     : 2511
SSH_AUTH_SOCK                     : *** redacted ***
TAR                               : /bin/tar
TERM                              : xterm-256color
USER                              : david
XAUTHORITY                        : /home/david/.Xauthority
XDG_CONFIG_DIRS                   : /etc/xdg/xdg-cinnamon:/etc/xdg
XDG_CURRENT_DESKTOP               : X-Cinnamon
XDG_DATA_DIRS                     : /usr/share/cinnamon:/usr/share/gnome:/home/david/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_GREETER_DATA_DIR              : /var/lib/lightdm-data/david
XDG_RUNTIME_DIR                   : /run/user/1000
XDG_SEAT                          : seat0
XDG_SEAT_PATH                     : /org/freedesktop/DisplayManager/Seat0
XDG_SESSION_DESKTOP               : cinnamon
XDG_SESSION_ID                    : c2
XDG_SESSION_PATH                  : /org/freedesktop/DisplayManager/Session0
XDG_SESSION_TYPE                  : x11
XDG_VTNR                          : 7

R Version
--------------------------------------------------
platform       : x86_64-pc-linux-gnu
arch           : x86_64
os             : linux-gnu
system         : x86_64, linux-gnu
status         : 
major          : 4
minor          : 1.2
year           : 2021
month          : 11
day            : 01
svn rev        : 81115
language       : R
version.string : R version 4.1.2 (2021-11-01)
nickname       : Bird Hippie

R Home
--------------------------------------------------
/usr/lib/R

R Search Path
--------------------------------------------------
.GlobalEnv       
tools:rstudio    
package:stats    
package:graphics 
package:grDevices
package:utils    
package:datasets 
package:methods  
Autoloads        
package:base     

R Library Paths
--------------------------------------------------
/home/david/R/x86_64-pc-linux-gnu-library/4.1
/usr/local/lib/R/site-library                
/usr/lib/R/site-library                      
/usr/lib/R/library                           

Loaded Packages
--------------------------------------------------
base      : /usr/lib/R/library/base     
compiler  : /usr/lib/R/library/compiler 
datasets  : /usr/lib/R/library/datasets 
graphics  : /usr/lib/R/library/graphics 
grDevices : /usr/lib/R/library/grDevices
methods   : /usr/lib/R/library/methods  
stats     : /usr/lib/R/library/stats    
tools     : /usr/lib/R/library/tools    
utils     : /usr/lib/R/library/utils    

Installed Packages
--------------------------------------------------
                 Package                                       LibPath    Version
1                  abind /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.4-5
2              animation /home/david/R/x86_64-pc-linux-gnu-library/4.1        2.7
3                    aqp /home/david/R/x86_64-pc-linux-gnu-library/4.1       1.40
4                askpass /home/david/R/x86_64-pc-linux-gnu-library/4.1        1.1
5              assertive /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3-6
6         assertive.base /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-9
7         assertive.code /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
8         assertive.data /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
9      assertive.data.uk /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
10     assertive.data.us /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
11   assertive.datetimes /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
12       assertive.files /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
13    assertive.matrices /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
14      assertive.models /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
15     assertive.numbers /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-2
16  assertive.properties /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-4
17  assertive.reflection /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-5
18        assertive.sets /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
19     assertive.strings /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
20       assertive.types /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.0-3
21            assertthat /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.2.1
22             backports /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.4.1
23             base64enc /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.1-3
24                BBmisc /home/david/R/x86_64-pc-linux-gnu-library/4.1       1.11
25                    BH /home/david/R/x86_64-pc-linux-gnu-library/4.1   1.78.0-0
26                   bit /home/david/R/x86_64-pc-linux-gnu-library/4.1      4.0.4
27                 bit64 /home/david/R/x86_64-pc-linux-gnu-library/4.1      4.0.5
28                bitops /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-7
29                  blob /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.2
30              blogdown /home/david/R/x86_64-pc-linux-gnu-library/4.1        1.7
31              bookdown /home/david/R/x86_64-pc-linux-gnu-library/4.1       0.24
32                  boot /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.3-28
33                  brew /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-6
34                  brio /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.3
35                 broom /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.7.11
36                 bslib /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.1
37                cachem /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.6
38                 callr /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.7.0
39           cameratrapr /home/david/R/x86_64-pc-linux-gnu-library/4.1 0.0.0.9000
40                   car /home/david/R/x86_64-pc-linux-gnu-library/4.1     3.0-12
41               carData /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.0-5
42                 caret /home/david/R/x86_64-pc-linux-gnu-library/4.1     6.0-90
43            cellranger /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.0
44             checkmate /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.0.0
45              circular /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.4-93
46              classInt /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.4-3
47                   cli /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.1.0
48                 clipr /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.7.1
49                  coda /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.19-4
50             codetools /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.2-18
51           collections /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.5
52            colorRamps /home/david/R/x86_64-pc-linux-gnu-library/4.1        2.3
53            colorspace /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.0-2
54            commonmark /home/david/R/x86_64-pc-linux-gnu-library/4.1        1.7
55               conquer /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.1
56              corrplot /home/david/R/x86_64-pc-linux-gnu-library/4.1       0.92
57               cowplot /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.1
58                 cpp11 /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.4.2
59                crayon /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.4.2
60           credentials /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.3.2
61             crosstalk /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.0
62                  crul /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.0
63                  curl /home/david/R/x86_64-pc-linux-gnu-library/4.1      4.3.2
64             cyclocomp /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.0
65            data.table /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.14.2
66              davidoff /home/david/R/x86_64-pc-linux-gnu-library/4.1 0.0.0.9000
67                   DBI /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.2
68                dbplyr /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.1.1
69                deldir /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-6
70              DEoptimR /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.0-10
71                  desc /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.4.0
72              devtools /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.4.3
73             dichromat /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.0-0
74               diffobj /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.5
75                digest /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.6.29
76                 dismo /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.3-5
77            doParallel /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.0.16
78             dotCall64 /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-1
79                 dplyr /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.7
80                dtplyr /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.0
81                 e1071 /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.7-9
82              ellipsis /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.2
83              evaluate /home/david/R/x86_64-pc-linux-gnu-library/4.1       0.14
84                 exifr /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.2
85                  expm /home/david/R/x86_64-pc-linux-gnu-library/4.1    0.999-6
86                 fansi /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.0
87                farver /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.1.0
88             fasterize /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.3
89               fastmap /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.0
90             fastmatch /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1-3
91              fasttime /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-2
92                fields /home/david/R/x86_64-pc-linux-gnu-library/4.1       13.3
93          fitdistrplus /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1-6
94                   FNN /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.3
95           fontawesome /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.2.2
96               forcats /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.5.1
97               foreach /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.5.1
98           forestError /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.0
99                    fs /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.5.2
100               future /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.23.0
101         future.apply /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.8.1
102               gargle /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.0
103            gdalUtils /home/david/R/x86_64-pc-linux-gnu-library/4.1    2.0.3.2
104            gdistance /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.3-6
105             generics /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.1.1
106              geojson /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.4
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327        spatstat.core /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.3-2
328        spatstat.data /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.1-2
329        spatstat.geom /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.3-1
330      spatstat.linnet /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.3-1
331      spatstat.sparse /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.1-0
332       spatstat.utils /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.3-0
333               spData /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.0.1
334                spdep /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2-1
335              splancs /home/david/R/x86_64-pc-linux-gnu-library/4.1    2.01-42
336              SQUAREM /home/david/R/x86_64-pc-linux-gnu-library/4.1     2021.1
337                stars /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.5-5
338              statmod /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.4.36
339       statnet.common /home/david/R/x86_64-pc-linux-gnu-library/4.1      4.5.0
340              stringi /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.7.6
341              stringr /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.4.0
342               styler /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.6.2
343             survival /home/david/R/x86_64-pc-linux-gnu-library/4.1     3.2-13
344              svglite /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.0.0
345               svMisc /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.3
346                  sys /home/david/R/x86_64-pc-linux-gnu-library/4.1        3.4
347          systemfonts /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.3
348               tensor /home/david/R/x86_64-pc-linux-gnu-library/4.1        1.5
349                terra /home/david/R/x86_64-pc-linux-gnu-library/4.1     1.4-22
350             testthat /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.1.1
351               tibble /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.1.6
352                tidyr /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.4
353           tidyselect /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.1.1
354            tidyverse /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.3.1
355             timeDate /home/david/R/x86_64-pc-linux-gnu-library/4.1   3043.102
356              tinytex /home/david/R/x86_64-pc-linux-gnu-library/4.1       0.36
357                 tmap /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.3-2
358            tmaptools /home/david/R/x86_64-pc-linux-gnu-library/4.1      3.1-1
359            triebeard /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.0
360                 tzdb /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.2.0
361                units /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.7-2
362             urltools /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.7.3
363              usethis /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.1.5
364                 utf8 /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.2.2
365                 uuid /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0-3
366                   V8 /home/david/R/x86_64-pc-linux-gnu-library/4.1      4.0.0
367                vctrs /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.8
368                velox /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.2.1
369              viridis /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.6.2
370          viridisLite /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.4.0
371                vroom /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.5.7
372                waldo /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.1
373              webshot /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.5.2
374              whisker /home/david/R/x86_64-pc-linux-gnu-library/4.1        0.4
375          widgetframe /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.3.1
376                withr /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.4.3
377                   wk /home/david/R/x86_64-pc-linux-gnu-library/4.1      0.6.0
378                 xfun /home/david/R/x86_64-pc-linux-gnu-library/4.1       0.29
379              xgboost /home/david/R/x86_64-pc-linux-gnu-library/4.1    1.5.0.2
380                  XML /home/david/R/x86_64-pc-linux-gnu-library/4.1   3.99-0.8
381                 xml2 /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.3.3
382         xmlparsedata /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.5
383                xopen /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.0.0
384               xtable /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.8-4
385                  xts /home/david/R/x86_64-pc-linux-gnu-library/4.1     0.12.1
386                 yaml /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.2.1
387                  zip /home/david/R/x86_64-pc-linux-gnu-library/4.1      2.2.0
388                  zoo /home/david/R/x86_64-pc-linux-gnu-library/4.1      1.8-9
389                 base                            /usr/lib/R/library      4.1.2
390                 boot                            /usr/lib/R/library     1.3-28
391                class                            /usr/lib/R/library     7.3-20
392              cluster                            /usr/lib/R/library      2.1.2
393            codetools                            /usr/lib/R/library     0.2-18
394             compiler                            /usr/lib/R/library      4.1.2
395             datasets                            /usr/lib/R/library      4.1.2
396              foreign                            /usr/lib/R/library     0.8-82
397             graphics                            /usr/lib/R/library      4.1.2
398            grDevices                            /usr/lib/R/library      4.1.2
399                 grid                            /usr/lib/R/library      4.1.2
400           KernSmooth                            /usr/lib/R/library    2.23-20
401              lattice                            /usr/lib/R/library    0.20-45
402                 MASS                            /usr/lib/R/library     7.3-55
403               Matrix                            /usr/lib/R/library      1.4-0
404              methods                            /usr/lib/R/library      4.1.2
405                 mgcv                            /usr/lib/R/library     1.8-38
406                 nlme                            /usr/lib/R/library    3.1-155
407                 nnet                            /usr/lib/R/library     7.3-17
408             parallel                            /usr/lib/R/library      4.1.2
409                rpart                            /usr/lib/R/library     4.1-15
410              spatial                            /usr/lib/R/library     7.3-11
411              splines                            /usr/lib/R/library      4.1.2
412                stats                            /usr/lib/R/library      4.1.2
413               stats4                            /usr/lib/R/library      4.1.2
414             survival                            /usr/lib/R/library     3.2-13
415                tcltk                            /usr/lib/R/library      4.1.2
416                tools                            /usr/lib/R/library      4.1.2
417                utils                            /usr/lib/R/library      4.1.2

R System Profile: /usr/lib/R/library/base/R/Rprofile
--------------------------------------------------
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).

### Copyright (C) 1995-2020 The R Core Team

### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).

.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version            # for S compatibility

## for backwards compatibility only
R.version.string <- R.version$version.string

## NOTA BENE: options() for non-base package functionality are in places like
##            --------- ../utils/R/zzz.R

options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="@CRAN@"))
# options(BIOC = "http://www.bioconductor.org")

## setting from an env variable added in 4.0.2
local({to <- as.integer(Sys.getenv("R_DEFAULT_INTERNET_TIMEOUT", 60))
    if (is.na(to) || to <= 0) to <- 60L
    options(timeout = to)
})
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in  ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'

if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
                                 "FALSE")))) {
    options(stringsAsFactors = FALSE)
} else {
    options(stringsAsFactors = TRUE)
}

if(!interactive() && is.null(getOption("showErrorCalls")))
    options(showErrorCalls = TRUE)

local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
       if(identical(dp, "")) ## it fact methods is done first
           dp <- c("datasets", "utils", "grDevices", "graphics",
                   "stats", "methods")
       else if(identical(dp, "NULL")) dp <- character(0)
       else dp <- strsplit(dp, ",")[[1]]
       dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace
       options(defaultPackages = dp)
    })

## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
           .expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
           .expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))

local({
    if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
        setSessionTimeLimit(cpu = tl)
    if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
        setSessionTimeLimit(elapsed = tl)
})

.First.sys <- function()
{
    for(pkg in getOption("defaultPackages")) {
        res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
                       character.only = TRUE)
        if(!res)
            warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
                    call. = FALSE, domain = NA)
    }
}

## called at C level in the startup process prior to .First.sys
.OptRequireMethods <- function()
{
    pkg <- "methods" # done this way to avoid R CMD check warning
    if(pkg %in% getOption("defaultPackages"))
        if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
                    character.only = TRUE))
            warning('package "methods" in options("defaultPackages") was not found',
                    call. = FALSE)
}

if(nzchar(Sys.getenv("R_BATCH"))) {
    .Last.sys <- function()
    {
        cat("> proc.time()\n")
        print(proc.time())
    }
    ## avoid passing on to spawned R processes
    ## A system has been reported without Sys.unsetenv, so try this
    try(Sys.setenv(R_BATCH=""))
}

local({
    if(nzchar(rv <- Sys.getenv("_R_RNG_VERSION_")))
        suppressWarnings(RNGversion(rv))
})

.sys.timezone <- NA_character_
.First <- NULL
.Last <- NULL
###-*- R -*- Unix Specific ----

.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nzchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ":"))
.Library.site <- .Library.site[file.exists(.Library.site)]

invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
                      unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
                      ))))
local({
    popath <- Sys.getenv("R_TRANSLATIONS", "")
    if(!nzchar(popath)) {
        paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
        popath <- dirname(paths[file.exists(paths)][1])
    }
    bindtextdomain("R", popath)
    bindtextdomain("R-base", popath)
    assign(".popath", popath, .BaseNamespaceEnv)
})
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
    lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
    papersize <- if(nchar(lcpaper))
        if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
    else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,
        printcmd = Sys.getenv("R_PRINTCMD"),
        dvipscmd = Sys.getenv("DVIPS", "dvips"),
        texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
        browser = Sys.getenv("R_BROWSER"),
        pager = file.path(R.home(), "bin", "pager"),
        pdfviewer = Sys.getenv("R_PDFVIEWER"),
        useFancyQuotes = TRUE)
})

## non standard settings for the R.app GUI of the macOS port
if(.Platform$GUI == "AQUA") {
    ## this is set to let RAqua use both X11 device and X11/TclTk
    if (Sys.getenv("DISPLAY") == "")
    Sys.setenv("DISPLAY" = ":0")

    ## this is to allow gfortran compiler to work
    Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"

## de-dupe the environment on macOS (bug in Yosemite which affects things like PATH)
if (grepl("^darwin", R.version$os)) local({
    ## we have to de-dupe one at a time and re-check since the bug affects how
    ## environment modifications propagate
    while(length(dupes <- names(Sys.getenv())[table(names(Sys.getenv())) > 1])) {
        env <- dupes[1]
        value <- Sys.getenv(env)
        Sys.unsetenv(env)             ## removes the dupes, good
        .Internal(Sys.setenv(env, value)) ## wrapper requries named vector, a pain, hence internal
    }
})

local({
    tests_startup <- Sys.getenv("R_TESTS")
    if(nzchar(tests_startup)) source(tests_startup)
})

R Site Profile: /usr/lib/R/etc/Rprofile.site
--------------------------------------------------
##                      Emacs please make this -*- R -*-
## empty Rprofile.site for R on Debian
##
## Copyright (C) 2008 - 2018  Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Rprofile and Rprofile.site

# ## Example of .Rprofile
# options(width=65, digits=5)
# options(show.signif.stars=FALSE)
# setHook(packageEvent("grDevices", "onLoad"),
#         function(...) grDevices::ps.options(horizontal=FALSE))
# set.seed(1234)
# .First <- function() cat("\n   Welcome to R!\n\n")
# .Last <- function()  cat("\n   Goodbye!\n\n")

# ## Example of Rprofile.site
# local({
#  # add MASS to the default packages, set a CRAN mirror
#  old <- getOption("defaultPackages"); r <- getOption("repos")
#  r["CRAN"] <- "http://my.local.cran"
#  options(defaultPackages = c(old, "MASS"), repos = r)
#})

## We set the cloud mirror, which is 'network-close' to everybody, as default
local({
    r <- getOption("repos")
    r["CRAN"] <- "https://cloud.r-project.org"
    options(repos = r)
})

R User Profile: /home/david/.Rprofile
--------------------------------------------------
(File does not exist)

R Site Environ: /usr/lib/R/etc/Renviron.site
--------------------------------------------------
##                      Emacs please make this -*- R -*-
## empty Renviron.site for R on Debian
##
## Copyright (C) 2008 - 2019  Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Renviron and Renviron.site

# ## Example ~/.Renviron on Unix
# R_LIBS=~/R/library
# PAGER=/usr/local/bin/less

# ## Example .Renviron on Windows
# R_LIBS=C:/R/library
# MY_TCLTK="c:/Program Files/Tcl/bin"

# ## Example of setting R_DEFAULT_PACKAGES (from R CMD check)
# R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'
# # this loads the packages in the order given, so they appear on
# # the search path in reverse order.

## # We comment out this line in the default Renviron, you can re-enable it here
## # @R_PLATFORM@ can be eg x86_64-pc-linux-gnu, see /etc/R/Renviron for R_PLATFORM
## # @MAJ_MIN_VERSION@ is likely something like '3.4', see /etc/R/Renviron too
## #
## # Also note that you set this per-user via '%p' and '%v' for platform and version
#R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM@-library/@MAJ_MIN_VERSION@'}

## edd May 2019
##
## Debian (and its derivatives) impose a set of compiler flags to prevent some known
## security issues with compiled code.  These flags then become defaults for R as well
## (see eg /etc/R/Makeconf) but nevertheless confuse R as warnings get triggers.  Users,
## on the other hand, are often stumped about these.  So with this variable we declare
## these options as known for the local checks on the machine this file is on.
##
## See Section 8 of the R Internals manual for many more options to customize tests.
_R_CHECK_COMPILATION_FLAGS_KNOWN_='-Wformat -Werror=format-security -Wdate-time'

R User Environ: /home/david/.Renviron
--------------------------------------------------
EARTHENGINE_INIT_MESSAGE="True"
EARTHENGINE_PYTHON="/home/david/miniconda3/envs/rgee/bin/python"
EARTHENGINE_ENV="rgee"

R Temporary Directory
--------------------------------------------------
/tmp/Rtmp7yFJwI

Files in R Temporary Directory
--------------------------------------------------
rs-graphics-2fa2c8ac-7547-4d38-a963-4a649e67054f

Log file: /home/david/.local/share/rstudio/log/rdesktop.log
--------------------------------------------------

(Not Found)

Log file: /home/david/.local/share/rstudio/log/rsession-david.log
--------------------------------------------------

2021-12-20T08:41:42.702645Z [rsession-david] WARNING FileLock classes not yet initialized; please call 'FileLock::initialize()' and 'FileLock::cleanUp()' as appropriate; LOGGED FROM: static bool rstudio::core::FileLock::verifyInitialized() src/cpp/core/file_lock/FileLock.cpp:113
2021-12-20T08:41:42.706216Z [rsession-david] ERROR system error 39 (Directory not empty) [path: /home/david/.rstudio-desktop/log, target-path: /home/david/.local/share/rstudio/log]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::move(const rstudio::core::FilePath&, rstudio::core::FilePath::MoveType, bool) const src/cpp/shared_core/FilePath.cpp:1392; LOGGED FROM: rstudio::core::Error rstudio::core::r_util::migrateUserStateIfNecessary(rstudio::core::r_util::SessionType) src/cpp/core/r_util/RUserData.cpp:154
2021-12-20T08:41:42.707915Z [rsession-david] WARNING Failed to migrate all user state from /home/david/.rstudio-desktop to /home/david/.local/share/rstudio; could not move log; LOGGED FROM: rstudio::core::Error rstudio::core::r_util::migrateUserStateIfNecessary(rstudio::core::r_util::SessionType) src/cpp/core/r_util/RUserData.cpp:176

User prefs: /home/david/.config/rstudio/rstudio-prefs.json
--------------------------------------------------

{
    "panes": {
        "quadrants": [
            "Source",
            "Console",
            "TabSet1",
            "TabSet2"
        ],
        "tabSet1": [
            "Environment",
            "History",
            "Connections",
            "Build",
            "VCS",
            "Presentation"
        ],
        "tabSet2": [
            "Files",
            "Plots",
            "Packages",
            "Help",
            "Viewer"
        ],
        "console_left_on_top": false,
        "console_right_on_top": true
    },
    "auto_detect_indentation": true,
    "editor_keybindings": "vim",
    "show_diagnostics_other": true,
    "save_files_before_build": true,
    "default_project_location": "~",
    "pdf_previewer": "rstudio",
    "document_author": "David",
    "wrap_tab_navigation": false,
    "reuse_sessions_for_project_links": true
}

System prefs: /etc/xdg/xdg-cinnamon:/etc/xdg/rstudio/rstudio-prefs.json
--------------------------------------------------

(Not Found)

User state: /home/david/.local/share/rstudio/rstudio-desktop.json
--------------------------------------------------

{
    "context_id": ""
}

[csaybar]

Hi @DavidDHofmann sorry for the late reply.

The problem looks to be related to reticulate rather than rgee or the earthengine-api. Are you able to run Python code from within Rstudio?

library(reticulate)
use_python("/home/david/miniconda3/envs/rgee/bin/python")
np <- import("numpy")
np$array([1, 2, 3])$reshape(1, 3)

[DavidDHofmann]

Hi @csaybar

The code does not work in R-Studio: Error: Unexpected '[' in "np$array([" However, the following piece of code runs:

library(reticulate)
use_python("/home/david/miniconda3/envs/rgee/bin/python")
np <- import("numpy", convert = F)
np$array(c(1, 2, 3))$reshape(1L, 3L)

Returning

[[1. 2. 3.]]

I've used reticulate in the past without any issues, so I'm not sure if this is the cause of the problem.

[csaybar]

Unfortunately, I'm not able to reproduce this issue. I will close this issue for now.