Closed vilhelmen closed 5 years ago
ocefpaf
commented
5 years ago Until we resolve #17 you need to install rgdal from the "old compiler label" like:
conda create --name TEST --channel conda-forge/label/cf201901 r-rgdalPing @isuruf and @mariusvniekerk for an example of the brokenness we have if we keep the cf201901 labeled packages on main.
vilhelmen
commented
5 years ago It works! Thank you so much, I've been going crazy trying to get this working.
vilhelmen
commented
5 years ago Or it did. Trying to get this to work with the existing environment makes conda decided that the only solution includes uninstalling conda. I have an old container I somehow got working by accident (I have never been able to replicate it), so I guess I'm just going to force everyone to use that one until #17 is finished.
dpryan79
commented
5 years ago vilhelmen
commented
5 years ago Thanks for the reminder. Booting up a container, here's what I got. Looks like something may be weird with proj?
waskd6@jupyter-waskd6:~/jupyter$ conda info
active environment : None
user config file : /home/waskd6/.condarc
populated config files : /opt/conda/.condarc
/home/waskd6/.condarc
conda version : 4.6.14
conda-build version : not installed
python version : 3.7.3.final.0
base environment : /opt/conda (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/conda/pkgs
/home/waskd6/.conda/pkgs
envs directories : /opt/conda/envs
/home/waskd6/.conda/envs
platform : linux-64
user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Linux/5.0.7-1.el7.elrepo.x86_64 ubuntu/18.04.2 glibc/2.27
UID:GID : 848809:848809
netrc file : None
offline mode : False## Package Plan ##
environment location: /opt/conda
added / updated specs:
- r-rgdal
The following packages will be downloaded:
package | build
---------------------------|-----------------
boost-cpp-1.68.0 | h11c811c_1000 20.5 MB conda-forge
freexl-1.0.5 | h14c3975_1002 43 KB conda-forge
geos-3.7.1 | hf484d3e_1000 1.6 MB conda-forge
geotiff-1.5.1 | he0d578f_1 275 KB conda-forge
giflib-5.1.7 | h516909a_1 455 KB conda-forge
hdf4-4.2.13 | h9a582f1_1002 952 KB conda-forge
json-c-0.13.1 | h14c3975_1001 71 KB conda-forge
kealib-1.4.10 | h1978553_1003 172 KB conda-forge
libdap4-3.19.1 | hd48c02d_1000 1.6 MB conda-forge
libgdal-2.4.1 | h1500935_2 18.2 MB conda-forge
libkml-1.3.0 | h328b03d_1009 637 KB conda-forge
libnetcdf-4.6.2 | hbdf4f91_1001 1.3 MB conda-forge
libspatialite-4.3.0a | h3360108_1027 3.1 MB conda-forge
openjpeg-2.3.1 | h58a6597_0 470 KB conda-forge
poppler-0.67.0 | h2fc8fa2_1002 8.8 MB conda-forge
poppler-data-0.4.9 | 1 3.4 MB conda-forge
proj4-6.0.0 | h765ec9c_0 9.2 MB conda-forge
r-rgdal-1.3_9 | r351h1b1f3b2_0 2.0 MB conda-forge
r-sp-1.3_1 |r351h96ca727_1000 1.9 MB conda-forge
xerces-c-3.2.2 | hac72e42_1001 3.3 MB conda-forge
------------------------------------------------------------
Total: 78.1 MB
The following NEW packages will be INSTALLED:
boost-cpp conda-forge/linux-64::boost-cpp-1.68.0-h11c811c_1000
freexl conda-forge/linux-64::freexl-1.0.5-h14c3975_1002
geos conda-forge/linux-64::geos-3.7.1-hf484d3e_1000
geotiff conda-forge/linux-64::geotiff-1.5.1-he0d578f_1
giflib conda-forge/linux-64::giflib-5.1.7-h516909a_1
hdf4 conda-forge/linux-64::hdf4-4.2.13-h9a582f1_1002
json-c conda-forge/linux-64::json-c-0.13.1-h14c3975_1001
kealib conda-forge/linux-64::kealib-1.4.10-h1978553_1003
libdap4 conda-forge/linux-64::libdap4-3.19.1-hd48c02d_1000
libgdal conda-forge/linux-64::libgdal-2.4.1-h1500935_2
libkml conda-forge/linux-64::libkml-1.3.0-h328b03d_1009
libnetcdf conda-forge/linux-64::libnetcdf-4.6.2-hbdf4f91_1001
libspatialite conda-forge/linux-64::libspatialite-4.3.0a-h3360108_1027
openjpeg conda-forge/linux-64::openjpeg-2.3.1-h58a6597_0
poppler conda-forge/linux-64::poppler-0.67.0-h2fc8fa2_1002
poppler-data conda-forge/noarch::poppler-data-0.4.9-1
proj4 conda-forge/linux-64::proj4-6.0.0-h765ec9c_0
r-rgdal conda-forge/linux-64::r-rgdal-1.3_9-r351h1b1f3b2_0
r-sp conda-forge/linux-64::r-sp-1.3_1-r351h96ca727_1000
xerces-c conda-forge/linux-64::xerces-c-3.2.2-hac72e42_1001
Proceed ([y]/n)? y
Downloading and Extracting Packages
poppler-0.67.0 | 8.8 MB | ################################################################################ | 100%
hdf4-4.2.13 | 952 KB | ################################################################################ | 100%
libkml-1.3.0 | 637 KB | ################################################################################ | 100%
kealib-1.4.10 | 172 KB | ################################################################################ | 100%
libdap4-3.19.1 | 1.6 MB | ################################################################################ | 100%
r-rgdal-1.3_9 | 2.0 MB | ################################################################################ | 100%
proj4-6.0.0 | 9.2 MB | ################################################################################ | 100%
libgdal-2.4.1 | 18.2 MB | ################################################################################ | 100%
geotiff-1.5.1 | 275 KB | ################################################################################ | 100%
giflib-5.1.7 | 455 KB | ################################################################################ | 100%
poppler-data-0.4.9 | 3.4 MB | ################################################################################ | 100%
freexl-1.0.5 | 43 KB | ################################################################################ | 100%
json-c-0.13.1 | 71 KB | ################################################################################ | 100%
xerces-c-3.2.2 | 3.3 MB | ################################################################################ | 100%
libnetcdf-4.6.2 | 1.3 MB | ################################################################################ | 100%
geos-3.7.1 | 1.6 MB | ################################################################################ | 100%
openjpeg-2.3.1 | 470 KB | ################################################################################ | 100%
r-sp-1.3_1 | 1.9 MB | ################################################################################ | 100%
libspatialite-4.3.0a | 3.1 MB | ################################################################################ | 100%
boost-cpp-1.68.0 | 20.5 MB | ################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
waskd6@jupyter-waskd6:~/jupyter$ gdalinfo --version
GDAL 2.4.1, released 2019/03/15
waskd6@jupyter-waskd6:~/jupyter$ R
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(rgdal)
Loading required package: sp
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/opt/conda/lib/R/library/rgdal/libs/rgdal.so':
libproj.so.13: cannot open shared object file: No such file or directory
>
Save workspace image? [y/n/c]: nYeah, it looks like there's some pinning that should happen.
Issue: Rgdal shared library issues
I've been trying to get rgdal working off and on for two weeks now and I've gotten nowhere because of so many different library issues (kea, gdal, poppler, now libssl). Here's the current environment before installing rgdal:
Environment (
conda list):Details about
condaand system (conda info):And here's the delta from installing r-rgdal:
For starters,
libssl.sois missing, which must have been satisfied by some other package in earlier install attempts:Installing
openssl=1.0.2pfixes that dependency, so that may be an issue for a different repo, but I don't have the bandwidth to hunt that down.Restarting with
r-rgdaland `openssl=1.0.2p' gets us the following delta:This starts the
libpopplerissues:Since
libpoppler's version number is off by about 11 from the package version (?????), I dig through Conda-forge packages, unpacking them and checking the lib version numbers manually and determine we need poppler 65 to getlibpoppler.so.76. Conda-forge has a mysterious gap where poppler 65 goes, but pkgs/main has it:This brings the install to
r-rgdal openssl=1.0.2p poppler=0.65.0and the delta to:Now this issue is
libkea.kealib1.4.9 was selected for some reason by conda. Now the install isr-rgdal openssl=1.0.2p poppler=0.65.0 kealib=1.4.7and the delta is (every reinstall is done in a fresh container):Then we hit the mystery zone where it stops working because ????????? and I haven't been able to get around it.
The symbol mentions kea, but also c++11, it could be either, both, or neither. Others online mention downgrading
libgdal, but most posts are either from 2014 or end with either "I changed a thing, try it again." "That works, thanks!" or "I fixed it, nevermind".In the end, you generally always end up an an undefined symbol in one of
libgdal,libpoppler,libkea, etc.Any help would be appreciated. I am clearly out of ideas.