Conda error parsing .yml file

Technical Support
12

So when I ran
source activate qiime2-2018.11

it went through all of the package installations but displayed this output:

Preparing transaction: done
Verifying transaction: done
Executing transaction: | Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK

done
Requirement already satisfied: msgpack==0.5.6 in /Users/rachael/ls/envs/qiime2-2018.11/lib/python3.5/site-packages (from -r /Users/rachael/qiime2/condaenv.8LDTwr.requiremen$
dyld: lazy symbol binding failed: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/rachael/ls/envs/qiime2-2018.11/lib/libpython3.5m.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/rachael/ls/envs/qiime2-2018.11/lib/libpython3.5m.dylib
  Expected in: "/usr/lib/libSystem.B.dylib


CondaValueError: pip returned an error

I was able to import the QIIME1 split_libary seqs.fna file as a .qza file:

qiime tools import --input-path seqs.fna --output-path seqs.qza --type SampleData[Sequences]

but when I tried to run dada2 (denoise-paired) I received this error:

Trace/BPT trap: 5

I looked this up on the forum and saw it connected with the first error I received after installation. I triple-checked that I was running the right version (my machine is a Mac) and even tried a OS X software update. However, it appears the machine is still running Maverick.

Do I need to update to at least 10.10 OSX? It looks like that's been an issue for others. Unfortunately I am ssh-ing into my bioinformatics machine so I used

sudo softwareupdate -iva

and it still says System Version: OS X 10.9.5 when i ran system_profiler SPSoftwareDataType.

Do you think this is stemming from an incompatibility with the older OS X version as it was with Lazy symbol binding failed - #23 by thermokarst?

If it is I will not be able to update until I can manually accessing the machine on Tuesday.

Thank you! :raccoon: