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snakemake needs r-base 3.5.1 but conda won't install. #17

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Jeltje opened this issue Nov 13, 2023 · 0 comments
Open

snakemake needs r-base 3.5.1 but conda won't install. #17

Jeltje opened this issue Nov 13, 2023 · 0 comments

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@Jeltje
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Jeltje commented Nov 13, 2023

I'm following the steps in README.md

When I do the dry run, there are lots of comments about missing output files (which seems to make sense), but no clear errors. But when I run the actual command
snakemake --use-conda --configfile config.yml -j 4
I get a long error tree about r-base 3.5.1, ending with

   ├─ r 3.5.1 would require
   │  └─ r-base >=3.5.1,<3.5.2.0a0  but there are no viable options
   │     ├─ r-base 3.5.1 would require
   │     │  └─ libuuid >=1.0.3,<2.0a0 , which conflicts with any installable versions previously reported;
   │     └─ r-base 3.5.1 conflicts with any installable versions previously reported;
   └─ r 3.5.1 conflicts with any installable versions previously reported.

r-base isn't listed in either environment.yaml or envs/SV.yml so the conda install is incomplete.
R is not installed on my system, and if I try to install it manually in the cadd.sv env , this happens:

conda install r-base=3.5.1

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                                                                 failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.34=0
  - python==3.9.9=h543edf9_0_cpython -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
  - r-base=3.5.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.34

my OS is Rocky Linux 9.1. This happened even after I installed r-base=3.5.1 in another conda env and put it in my $PATH.

What do I do next?

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