bp-analyze misbehavior

[Douglas Theobald]

Hi Ben,

I have the latest bali-phy v 3.6.0 running on mac os mojave 10.14.6.  When I run bp-analyze on three chains, it no longer behaves as it did in earlier versions.  This is the screen output:

Creating new directory Results/ for summary files.

Summarizing distribution of numerical parameters: done.

Analyzing scalar variables: done.

Summarizing topology distribution:  done.

Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done.

Generate mixing diagnostics for topologies ...command: '/usr/local/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence1-PP.svg' 'Results/convergence2-PP.svg' < '/usr/local/lib/bali-phy/libexec/compare-runs2.R'

 exit: 1

In the Results/ directory, there is no longer an index.html file, nor are there alignment files of any sort.  This problem is not particular to a single dataset, but is the same for several different analyses I have done with widely varying sequence numbers and lengths.  Any advice you can give me?  

Many thanks,

Douglas

[Benjamin Redelings]

Hi Douglas,

Thanks for the bug report -- it looks like one of the sub-commands is crashing and stopping the bp-analyze analysis.

Its probably the compare-runs2.R script, but can you send me the file `Results/commands.log`?  That should show all the commands.  Then we need to figure out what's wrong.

Also, if you following command from the parent directory of `Results`, what does it say?

'/usr/local/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence1-PP.svg' 'Results/convergence2-PP.svg' < '/usr/local/lib/bali-phy/libexec/compare-runs2.R'

-BenRI

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[Douglas Theobald]

Hi Ben,

Thanks for looking into this. I think you are right, in the commands.log file the last command crashes, and it's the one you suspect. The output is:

Error in svg(file = outfile1, height = 3, width = 7) :
svg: Cairo-based devices are not available for this platform
Execution halted

I looked a bit into this and it seems Cairo doesn't work on M1 ARM based Macs. I've attached the full commands.log also.

Cheers,

Douglas

[Benjamin Redelings]

Hi Douglas,

Interesting ... that's unfortunately that SVG is unavailable for some platforms!  I wonder if it is also unavailable for gnuplot on M1 ARM based Macs.

Hmm... I will look into modifying bp-analyze to fall back to PNGs if SVG doesn't work.  I should also make it a bit more fault-tolerant -- it shouldn't completely fail even if some images cannot be generated.  However, it will probably take me a few days to look at that.

-BenRI

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