biology/hyphy: Update to 2.5.52

[jrm]

Summary

FEL test is now passing, so remove comment about it failing.

Changes: https://github.com/veg/hyphy/releases/tag/2.5.52
Sponsored by: The FreeBSD Foundation

[jrm]

@fuz, could you test this on armv7. The patch you added in b27d05a94c645a3ba02c50122a229c37bec42559 no longer applies.

[fuz]

Build test passes on armv7 FreeBSD 13.2. Test suite fails partially:

[  0% 1/1] cd /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.52 && /usr/local/bin/ctest --force-new-ctest-process
Test project /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.52
      Start  1: UNIT-TESTS
 1/20 Test  #1: UNIT-TESTS .......................   Passed   10.54 sec
      Start  2: CODON
 2/20 Test  #2: CODON ............................***Exception: SegFault  0.11 sec
      Start  3: PROTEIN
 3/20 Test  #3: PROTEIN ..........................   Passed   44.58 sec
      Start  4: MTCODON
 4/20 Test  #4: MTCODON ..........................***Exception: SegFault  3.84 sec
      Start  5: ALGAE
 5/20 Test  #5: ALGAE ............................***Exception: SegFault  1.42 sec
      Start  6: CILIATES
 6/20 Test  #6: CILIATES .........................***Exception: SegFault  0.90 sec
      Start  7: SLAC
 7/20 Test  #7: SLAC .............................***Exception: SegFault  0.69 sec
      Start  8: SLAC-PARTITIONED
 8/20 Test  #8: SLAC-PARTITIONED .................***Exception: SegFault  1.09 sec
      Start  9: FEL
 9/20 Test  #9: FEL ..............................***Exception: SegFault  0.83 sec
      Start 10: MEME
10/20 Test #10: MEME .............................***Exception: SegFault  1.36 sec
      Start 11: MEME-PARTITIONED
11/20 Test #11: MEME-PARTITIONED .................***Exception: SegFault  1.95 sec
      Start 12: BUSTED
12/20 Test #12: BUSTED ...........................***Exception: SegFault  0.86 sec
      Start 13: BUSTED-SRV
13/20 Test #13: BUSTED-SRV .......................***Exception: SegFault  1.48 sec
      Start 14: RELAX
14/20 Test #14: RELAX ............................***Exception: SegFault  0.95 sec
      Start 15: FUBAR
15/20 Test #15: FUBAR ............................***Exception: SegFault  0.75 sec
      Start 16: BGM
16/20 Test #16: BGM ..............................***Exception: SegFault  0.84 sec
      Start 17: CONTRAST-FEL
17/20 Test #17: CONTRAST-FEL .....................***Exception: SegFault  0.71 sec
      Start 18: GARD
18/20 Test #18: GARD .............................   Passed   15.84 sec
      Start 19: FADE
19/20 Test #19: FADE .............................   Passed   93.63 sec
      Start 20: ABSREL
20/20 Test #20: ABSREL ...........................***Exception: SegFault  1.12 sec

20% tests passed, 16 tests failed out of 20

Total Test time (real) = 183.64 sec

The following tests FAILED:
          2 - CODON (SEGFAULT)
          4 - MTCODON (SEGFAULT)
          5 - ALGAE (SEGFAULT)
          6 - CILIATES (SEGFAULT)
          7 - SLAC (SEGFAULT)
          8 - SLAC-PARTITIONED (SEGFAULT)
          9 - FEL (SEGFAULT)
         10 - MEME (SEGFAULT)
         11 - MEME-PARTITIONED (SEGFAULT)
         12 - BUSTED (SEGFAULT)
         13 - BUSTED-SRV (SEGFAULT)
         14 - RELAX (SEGFAULT)
         15 - FUBAR (SEGFAULT)
         16 - BGM (SEGFAULT)
         17 - CONTRAST-FEL (SEGFAULT)
         20 - ABSREL (SEGFAULT)
Errors while running CTest

[jrm]

Thanks for testing. Unless you have some insight on how to fix the armv7 segfaults, I propose that I mark it as broken on armv7 and those crazy enough to want to run hyphy's computationally intense models of evolution on armv7 can submit an upstream bug report.