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plmdca.jl's Issues

Installation instructions miss dependencies

When I tried to install PlmDCA on a clean installation of Julia 1.4 according to the instructions in the README.md, I got the following error:
"
ERROR: Unsatisfiable requirements detected for package GaussDCA [bc09176e]:
GaussDCA [bc09176e] log:
├─GaussDCA [bc09176e] has no known versions!
└─restricted to versions * by PlmDCA [06784e46] — no versions left
└─PlmDCA [06784e46] log:
├─possible versions are: 0.1.0 or uninstalled
└─PlmDCA [06784e46] is fixed to version 0.1.0
"
The problem was fixed by installing GaussDCA. It would be helpful to add the dependencies to the README.

plmdca_sym produces bus error (core dumped)

This happens to me on Debian buster with Linux 5.10.4-arch2-1 and julia v1.5.3.

I have no issues running the Asymmetrical.

julia> plmdca_sym("pf14short.fasta")
removing duplicate sequences... done: 1000 -> 879
theta = 0.353373570449757 threshold = 18.0
M = 879 N = 53 Meff = 550.9766636141637
pl = 161.35968919934206
pl = 129.83936579535234
pl = 107.55717373668888
pl = 99.97858074552735
pl = 94.08066003325501
pl = 93.26876309424811
pl = 84.98602351594282
pl = 81.84495445732358
pl = 76.95332734021117
pl = 72.28205930537428
pl = 64.91695275894219
pl = 63.18811624018254
pl = 58.788056459710376
pl = 57.54192511000855

signal (7): Bus error
in expression starting at REPL[3]:1
unknown function (ip: 0x7f833f61ba49)
unsafe_copyto! at ./array.jl:293 [inlined]
_copyto_impl! at ./array.jl:335
copyto! at ./array.jl:326 [inlined]
copyto! at ./array.jl:350 [inlined]
copyto! at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/SharedArrays/src/SharedArrays.jl:587 [inlined]
SharedArray at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/SharedArrays/src/SharedArrays.jl:358 [inlined]
like_grad! at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:133
#19 at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:69
unknown function (ip: 0x7f830125cf46)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
nlopt_callback_wrapper at /root/.julia/packages/NLopt/hHfvt/src/NLopt.jl:387
unknown function (ip: 0x7f83012552f8)
luksan_plis at /root/.julia/artifacts/b6b3a6b7407f80385d7dd00275aa41d78e39abd9/lib/libnlopt.so (unknown line)
nlopt_optimize at /root/.julia/artifacts/b6b3a6b7407f80385d7dd00275aa41d78e39abd9/lib/libnlopt.so (unknown line)
optimize! at /root/.julia/packages/NLopt/hHfvt/src/NLopt.jl:578 [inlined]
optimize at /root/.julia/packages/NLopt/hHfvt/src/NLopt.jl:585 [inlined]
macro expansion at ./timing.jl:233 [inlined]
MinimizePLSym at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:70
#plmdca_sym#15 at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:29
plmdca_sym at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:18 [inlined]
#plmdca_sym#18 at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:49
plmdca_sym at /root/.julia/packages/PlmDCA/CNq5B/src/plmdca_sym.jl:48
unknown function (ip: 0x7f830125c6c2)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2231 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:117
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:206
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:157 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:566
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:660
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:840
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:790
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:883
eval at ./boot.jl:331
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
eval_user_input at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:134
repl_backend_loop at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:195
start_repl_backend at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:180
#run_repl#37 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:292
run_repl at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:288
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2231 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
#807 at ./client.jl:399
jfptr_YY.807_45002.clone_1 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:655
jl_f__apply_latest at /buildworker/worker/package_linux64/build/src/builtins.c:705
#invokelatest#1 at ./essentials.jl:710 [inlined]
invokelatest at ./essentials.jl:709 [inlined]
run_main_repl at ./client.jl:383
exec_options at ./client.jl:313
_start at ./client.jl:506
jfptr__start_53898.clone_1 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
unknown function (ip: 0x401931)
unknown function (ip: 0x401533)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4015d4)
Allocations: 54010554 (Pool: 53955138; Big: 55416); GC: 63
Bus error (core dumped)

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