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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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Fail to use r-spocc due to geos 3.6.2 recipe pb #10968

Open yvanlebras opened 6 years ago

yvanlebras commented 6 years ago

Hi everyone, Sorry if it's not the good place and/or if my issue is not well described....

I use the r-spocc recipe for Galaxy spocc tool and since several weeks, execution of this Galaxy tools fails with this stderr:

Fatal error: Exit code 1 ()
Error: package or namespace load failed for ‘spocc’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/tool_deps/_conda/envs/__r-spocc@0.8.0/lib/R/library/rgeos/libs/rgeos.so':
  libgeos-3.6.2.so: cannot open shared object file: No such file or directory
Execution halted

Unfortunately (and please excuse me for that ;) ) I'm not a conda-man, but I just try this week to debug the issue by my self and... I think I found the origin...

Looking at the meta.yaml file from the spocc conda package, it seems that the specified geos dependency is geos 3.6.2 hfc679d8_2 but looking at my installed galaxy tool dependency, the only libgeos I see is libgeos-3.6.3.so... copying/pasting (I know, this is not good but I'm a biologist ;) ) this libgeos-3.6.3.so in libgeos-3.6.2.so solve the Galaxy tool execution problem.... So I think the error is related to the geos 3.6.2 hfc679d8_2 conda recipe who don't install the good source ?

Please, don't hesitate to comment / ask things as I'm really not familiar with this.

dpryan79 commented 5 years ago

The cause of this is likely that r-geos isn't pinned to the version of libgeos it's getting compiled against https://github.com/conda-forge/r-rgeos-feedstock/blob/master/recipe/meta.yaml#L42

Since things are slowly getting rebuilt for R 3.5.1, creating an issue on r-geos would probably be wise, since this can be fixed during the next build bump.