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philarevalo / PopCOGenT

Microbial Populations as Clusters Of Gene Transfer
GNU General Public License v3.0
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Issue with R on phybreak4 #24

Closed Elcquid closed 1 year ago

Elcquid commented 3 years ago

When I run phybreak4.retreiveLikelihood.py, I get the following:

PopCOGenT) connolly_j_husky_neu_edu@popcogent:/extra-space/home/PopCOGenT/src/core_gene_sweeps$ python3 phybreak4.retrieveLikelihood.py /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information available (required by /lib/x86_64-linux-gnu/libncursesw.so.5) /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/R: /home/connolly_j_husky_neu_edu/.conda/envs/PopCOGenT/lib/R/bin/exec/../../lib/../../libtinfo.so.6: no version information availabble (required by /lib/x86_64-linux-gnu/libncursesw.so.5) Fatal error: cannot open file 'phybreak.leafdist_compare.R': No such file or directory

It looks like some kind of versioning problem, but I haven't been able to resolve it. Any advice?

Elcquid commented 3 years ago

I noticed that phybreak.leafdist_compare.R actually does exist, so I decided to just run it separately, and it throws a similar warning, but seems to work. Perhaps the version problem and the fatal error are unrelated.