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Cannot find proj.db #19

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sgvignali opened this issue Mar 31, 2023 · 7 comments
Closed

Cannot find proj.db #19

sgvignali opened this issue Mar 31, 2023 · 7 comments

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@sgvignali
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Using the method described in #17 some libraries are missing. Below the R code to reproduce the error:

library(ggplot2)
library(rnaturalearth)

map <- ne_countries(scale = "medium",
                    type = "countries",
                    continent = "Europe",
                    returnclass = "sf")

ggplot(data = map,
       mapping = aes(fill = pop_est)) +
  geom_sf(size = 0.1)

Not always, but often, there is the following warning:

Warning message:
In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory

I guess because the libudunits2-dev library is not installed.

Moreover, there is the following error:

Error: C stack usage  7977892 is too close to the limit
In addition: There were 50 or more warnings (use warnings() to see the first 50)

and the output of warnings() is:

Warning messages:
1: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
2: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
3: In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory
4: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
5: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
6: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
7: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
8: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
9: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
10: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
11: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
12: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
13: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
14: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
15: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
16: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
17: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
18: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
19: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
20: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
21: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
22: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
23: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
24: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
25: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
26: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
27: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
28: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
29: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
30: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
31: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
32: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
33: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
34: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
35: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
36: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
37: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
38: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
39: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
40: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
41: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
42: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
43: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
44: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
45: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
46: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
47: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
48: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
49: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
50: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
@Enchufa2
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Enchufa2 commented Apr 1, 2023 •
edited

Not always, but often, there is the following warning:

Warning message:
In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory

I guess because the libudunits2-dev library is not installed.

I have no idea where this warning comes from, but it has nothing to do with udunits2. It is installed and it works just fine.

Moreover, there is the following error:

Error: C stack usage  7977892 is too close to the limit
In addition: There were 50 or more warnings (use warnings() to see the first 50)

and the output of warnings() is:

Warning messages:
1: In CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create_from_database: Cannot find proj.db
...

Now it seems that the proj database is not found. This is a problem. :-\

@Enchufa2
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Enchufa2 commented Apr 1, 2023

According to PROJ's docs, ../share/proj is automatically found if the installation respects the build structure, which Ubuntu doesn't, placing the library in a subfolder. So another way is by setting PROJ_LIB, or PROJ_DATA for version 9.1 and above. In this container, there's version 8, so setting

ENV PROJ_LIB /home/rstudio/.local/share/R/rspm/usr/share/proj

solves the issue. Not sure how to address this from rspm.

@Enchufa2
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Enchufa2 commented Apr 1, 2023

About the R_X11.so warning, I see the same warning with any ggplot2 chart on top of the base image, so it's an issue of the base image.

@Enchufa2 Enchufa2 changed the title Missing libraries Cannot find proj.db Apr 1, 2023
@sgvignali
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For the R_X11.so warning the missing library is libxt6, if you install it manually the warning disappears.

@sgvignali
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Is it possible to fix this?

@Enchufa2
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Enchufa2 commented Apr 14, 2023 •
edited

I'm not sure. I still have to investigate further. But with the root mode you shouldn't have this issue, at least in containers.

@Enchufa2
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Enchufa2 commented Apr 14, 2023 •
edited

It seems that moving all the libs up one level (to the standard directory) fixes the issue.

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@Enchufa2 @sgvignali