Comments (14)
MatthieuStigler
commented on July 18, 2024
1
got you, sorry about that: this is on focal 20.04
from r2u.
MatthieuStigler
commented on July 18, 2024
1
sounds good, thanks for your insights!
from r2u.
eddelbuettel
commented on July 18, 2024
@MatthieuStigler Can we start at the top please: Which of the two containers did you use?
First off, builds are incremental: if a package is updated, we get the version of that package as it is then. We do not control library versions.
Second, builds are somewhat "unpredictable" in the sense that most package rely on the underlying RSPM/PPM binary. But just to make everybody's life a bit more, maybe 2% or 3% packages comes as source because RSPM/PPM in their magic does not / cannot build it. At that point I build it from source. But it is bloody hard to align it with RSPM/PPM builds I have no control over.
(Third, BioConductor is always from source.)
So in short if something fails let me know and I can maybe rebuild. If it merely warns that is maybe not worth the effort. Overall maybe we need a 'census' for some packages to ensure they all have consistent library versions. Maybe the geospatial community has such a script.
from r2u.
MatthieuStigler
commented on July 18, 2024
Mmh, not sure what are the containers, I am using it here without a Docker infrastructure, just on my machine (using https://dirk.eddelbuettel.com/cranapt). So I guess yes it is difficult to make the example fully reproducible?
Regarding the gravity of the problem, it is hard to tell, so far I encountered quite a few warnings due to the versions mismatch. Given how central sf is to my workflow and how often the warnings appeared, I felt I wanted to make sure they would not appear again.
I don't have any understanding of the RSPM/PPM, but is it possible that sf requires re-compilation whenever rgeos/rgdal are updated, even if sf itself is not updated?
Thanks!!
from r2u.
eddelbuettel
commented on July 18, 2024
So substitute 'container flavour' for 'Ubuntu flavour': You haven't told me if the 'issue' arose under focal or jammy.
from r2u.
eddelbuettel
commented on July 18, 2024
That was the first. Jammy may be smoother so I would try that.
Overall, and as you describe above, "it's tricky". So at this stage the best we can probably do is catalog it. And/or add some helper scripts to catalogue versions. We can of course query apt too. Do you want to poke around a little?
from r2u.
MatthieuStigler
commented on July 18, 2024
Fair point, I should update at some point.
Mmh, if this is tricky for you, it will be even more for me. I am afraid that besides reporting it, I can't be of much help since I don't know about ppm nor cataloguing :-( I hope at least this post can be useful for later discoverability, if other users encounter the same issue and want to get rid of the warning running bspm::disable(); install.packages(c("sf")).
from r2u.
eddelbuettel
commented on July 18, 2024
Pretty straightforward: RSPM/PPM is where we get (most) pre-compiled (non .deb) packages from, this is documented. We then turn those into r-cran-* with full dependencies depending on what was compiled into them. So to some extend what "they do here" matters which is why I pointed you here.
Cataloguing: That was just shorthand for available.packages() and installed.packages() and friens.
And yes, a local install can always be your local fix. I think I close this now as there is no imminent issue for r2u.
from r2u.
eddelbuettel
commented on July 18, 2024
Keep me posted if/when you see 'odd' error or warning messages. I think sometimes these may be normal / expected, sometimes they may hint at something. I do build BioConductor in bulk because of their release schedule. Maybe if a few geospatial r2u users stick their heads together we can come up with a 'schema' to do something better (if and when we think it;s needed).
from r2u.
MatthieuStigler
commented on July 18, 2024
Just for further info, a quick example where non-updated sf might actually lead to an error. Note that I have sudo apt update with no pending updates (though update.packages() shows further available packages).
library(sf)
#> Linking to GEOS 3.10.2, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE
#> WARNING: different compile-time and runtime versions for GEOS found:
#> Linked against: 3.10.2-CAPI-1.16.0 compiled against: 3.8.0-CAPI-1.13.1
#> It is probably a good idea to reinstall sf, and maybe rgeos and rgdal too
dang::shadowedPackages()
#> Package LibPath
#> 1: bspm /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 2: bspm /usr/local/lib/R/site-library
#> 3: dang /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 4: dang /usr/lib/R/site-library
#> 5: effects /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 6: effects /usr/lib/R/site-library
#> 7: maps /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 8: maps /usr/lib/R/site-library
#> 9: pryr /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 10: pryr /usr/lib/R/site-library
#> Version n good
#> 1: <package_version[1]> 2 TRUE
#> 2: <package_version[1]> 2 FALSE
#> 3: <package_version[1]> 2 TRUE
#> 4: <package_version[1]> 2 FALSE
#> 5: <package_version[1]> 2 TRUE
#> 6: <package_version[1]> 2 FALSE
#> 7: <package_version[1]> 2 TRUE
#> 8: <package_version[1]> 2 TRUE
#> 9: <package_version[1]> 2 TRUE
#> 10: <package_version[1]> 2 TRUE
st_crs("ESRI:102033")
#> Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ:
#> proj_create_from_database: SQLite error on SELECT name,
#> coordinate_system_auth_name, coordinate_system_code, geodetic_crs_auth_name,
#> geodetic_crs_code, conversion_auth_name, conversion_code,
#> area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM
#> projected_crs WHERE auth_name = ? AND code = ?: no such column:
#> area_of_use_auth_name
#> Error in st_crs.character("ESRI:102033"): invalid crs: ESRI:102033Created on 2023-02-24 with reprex v2.0.2
bspm::disable()
install.packages(c("sf", "rgeos"))
#> Installing packages into '/home/mstigler/R/x86_64-pc-linux-gnu-library/4.2'
#> (as 'lib' is unspecified)
library(sf)
#> Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.0; sf_use_s2() is TRUE
dang::shadowedPackages()
#> Package LibPath
#> 1: bspm /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 2: bspm /usr/local/lib/R/site-library
#> 3: dang /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 4: dang /usr/lib/R/site-library
#> 5: effects /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 6: effects /usr/lib/R/site-library
#> 7: maps /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 8: maps /usr/lib/R/site-library
#> 9: pryr /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 10: pryr /usr/lib/R/site-library
#> 11: rgeos /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 12: rgeos /usr/lib/R/site-library
#> 13: sf /home/mstigler/R/x86_64-pc-linux-gnu-library/4.2
#> 14: sf /usr/lib/R/site-library
#> Version n good
#> 1: <package_version[1]> 2 TRUE
#> 2: <package_version[1]> 2 FALSE
#> 3: <package_version[1]> 2 TRUE
#> 4: <package_version[1]> 2 FALSE
#> 5: <package_version[1]> 2 TRUE
#> 6: <package_version[1]> 2 FALSE
#> 7: <package_version[1]> 2 TRUE
#> 8: <package_version[1]> 2 TRUE
#> 9: <package_version[1]> 2 TRUE
#> 10: <package_version[1]> 2 TRUE
#> 11: <package_version[1]> 2 TRUE
#> 12: <package_version[1]> 2 TRUE
#> 13: <package_version[1]> 2 TRUE
#> 14: <package_version[1]> 2 TRUE
st_crs("ESRI:102033")
#> Coordinate Reference System:
#> User input: ESRI:102033
#> wkt:
#> PROJCRS["South_America_Albers_Equal_Area_Conic",
#> BASEGEOGCRS["SAD69",
#> DATUM["South American Datum 1969",
#> ELLIPSOID["GRS 1967 Modified",6378160,298.25,
#> LENGTHUNIT["metre",1]]],
#> PRIMEM["Greenwich",0,
#> ANGLEUNIT["Degree",0.0174532925199433]]],
#> CONVERSION["South_America_Albers_Equal_Area_Conic",
#> METHOD["Albers Equal Area",
#> ID["EPSG",9822]],
#> PARAMETER["Latitude of false origin",-32,
#> ANGLEUNIT["Degree",0.0174532925199433],
#> ID["EPSG",8821]],
#> PARAMETER["Longitude of false origin",-60,
#> ANGLEUNIT["Degree",0.0174532925199433],
#> ID["EPSG",8822]],
#> PARAMETER["Latitude of 1st standard parallel",-5,
#> ANGLEUNIT["Degree",0.0174532925199433],
#> ID["EPSG",8823]],
#> PARAMETER["Latitude of 2nd standard parallel",-42,
#> ANGLEUNIT["Degree",0.0174532925199433],
#> ID["EPSG",8824]],
#> PARAMETER["Easting at false origin",0,
#> LENGTHUNIT["metre",1],
#> ID["EPSG",8826]],
#> PARAMETER["Northing at false origin",0,
#> LENGTHUNIT["metre",1],
#> ID["EPSG",8827]]],
#> CS[Cartesian,2],
#> AXIS["(E)",east,
#> ORDER[1],
#> LENGTHUNIT["metre",1]],
#> AXIS["(N)",north,
#> ORDER[2],
#> LENGTHUNIT["metre",1]],
#> USAGE[
#> SCOPE["Not known."],
#> AREA["South America"],
#> BBOX[-60,-90,15,-30]],
#> ID["ESRI",102033]]Created on 2023-02-24 with reprex v2.0.2
from r2u.
eddelbuettel
commented on July 18, 2024
I just did
$ docker run --rm -ti eddelbuettel/r2u:jammy
# install.r sf rgeos
.... omitting output here ...
root@409741feb9cb:/# R -q
> library(sf)
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
> library(rgeos)
Loading required package: sp
rgeos version: 0.6-1, (SVN revision 692)
GEOS runtime version: 3.10.2-CAPI-1.16.0
Please note that rgeos will be retired during 2023,
plan transition to sf functions using GEOS at your earliest convenience.
GEOS using OverlayNG
Linking to sp version: 1.5-1
Polygon checking: TRUE
>
So in short I do not see a problem. Am I missing something?
from r2u.
MatthieuStigler
commented on July 18, 2024
oh sorry, I am not familiar with docker, I will make sure to use that when reporting further issues.
from r2u.
eddelbuettel
commented on July 18, 2024
It's just a simple way to "start from scratch" on a clean slate to check the versions in the repo as opposed to whatever I may have hanging around. And it is fast. Has many things going for it.
from r2u.
eddelbuettel
commented on July 18, 2024
You also have a old version of the dang function because it does not print the version numbers right in your example above. A while back I injected an explicit format() to ensure it does.
from r2u.
Related Issues (20)
- Instructions about installing bspm for r2u may be assuming a dependency that may be missing HOT 3
- Are certain Bioconductor packages out of date? HOT 4
- devEMF has graphics API version mismatch with current R HOT 1
- pandoc missing when installing rmarkdown HOT 2
- Alternative mirrors? HOT 4
- Different number of CRAN packages with `available.packages()`? HOT 6
- typical time lag for updating package versions? HOT 4
- Possible package missing from repo: r-cran-r2rtf HOT 6
- apt pinning seems to have no effect for r-cran-jquerylib HOT 15
- Problem with running install.packages() HOT 26
- Requesting 79 Bioconductor packages HOT 9
- Please update 10 CRAN packages and 1 Bioconductor package HOT 5
- Support for the ARM64 system architecture HOT 5
- Enhancement: Timeline for support of Ubuntu 24.04LTS? HOT 3
- Enhancement: Update to R 4.4 HOT 5
- Problems with R 4.4 and BiocManager HOT 2
- Error on installing stringi HOT 4
- Cannot install github packages when using r2u HOT 9
- controlling package versions / snaphots / reproducibility / mirroring HOT 2
- package âXMLâ was built under R version 4.4.0 HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
đ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. đđđ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google â¤ď¸ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from r2u.