If you think that there is an error in how your package is being tested or represented, please file an issue at NewPkgEval.jl, making sure to read the FAQ first.
Results with Julia v1.2.0
Testing was successful.
Last evaluation was ago and took 4 minutes, 45 seconds.
Resolving package versions...
Installed URIParser ───────────── v0.4.0
Installed Blosc ───────────────── v0.5.1
Installed Libz ────────────────── v1.0.0
Installed MbedTLS ─────────────── v0.7.0
Installed HDF5 ────────────────── v0.12.5
Installed CPLEX ───────────────── v0.6.1
Installed BinaryProvider ──────── v0.5.8
Installed COBRA ───────────────── v0.3.0
Installed Compat ──────────────── v2.2.0
Installed OrderedCollections ──── v1.1.0
Installed JSON ────────────────── v0.21.0
Installed MathProgBase ────────── v0.7.7
Installed Parsers ─────────────── v0.3.10
Installed HTTP ────────────────── v0.8.8
Installed IniFile ─────────────── v0.5.0
Installed MAT ─────────────────── v0.6.0
Installed Parameters ──────────── v0.12.0
Installed BufferedStreams ─────── v1.0.0
Installed CMake ───────────────── v1.1.2
Installed MathOptInterface ────── v0.9.7
Installed GLPK ────────────────── v0.12.0
Installed GLPKMathProgInterface ─ v0.4.4
Installed CMakeWrapper ────────── v0.2.3
Installed BenchmarkTools ──────── v0.4.3
Installed BinDeps ─────────────── v0.8.10
Updating `~/.julia/environments/v1.2/Project.toml`
[58298e0b] + COBRA v0.3.0
Updating `~/.julia/environments/v1.2/Manifest.toml`
[6e4b80f9] + BenchmarkTools v0.4.3
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[a74b3585] + Blosc v0.5.1
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[58298e0b] + COBRA v0.3.0
[a076750e] + CPLEX v0.6.1
[34da2185] + Compat v2.2.0
[60bf3e95] + GLPK v0.12.0
[3c7084bd] + GLPKMathProgInterface v0.4.4
[f67ccb44] + HDF5 v0.12.5
[cd3eb016] + HTTP v0.8.8
[83e8ac13] + IniFile v0.5.0
[682c06a0] + JSON v0.21.0
[2ec943e9] + Libz v1.0.0
[23992714] + MAT v0.6.0
[b8f27783] + MathOptInterface v0.9.7
[fdba3010] + MathProgBase v0.7.7
[739be429] + MbedTLS v0.7.0
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[30578b45] + URIParser v0.4.0
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building MbedTLS → `~/.julia/packages/MbedTLS/a1JFn/deps/build.log`
Building CPLEX ──→ `~/.julia/packages/CPLEX/iAQQk/deps/build.log`
┌ Error: Error building `CPLEX`:
│ ERROR: LoadError: Unable to locate CPLEX installation. Note this must be downloaded separately. See the CPLEX.jl README for further instructions.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] try_local_installation() at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:64
│ [3] top-level scope at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:86
│ [4] include at ./boot.jl:328 [inlined]
│ [5] include_relative(::Module, ::String) at ./loading.jl:1094
│ [6] include(::Module, ::String) at ./Base.jl:31
│ [7] include(::String) at ./client.jl:431
│ [8] top-level scope at none:5
│ in expression starting at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:77
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/backwards_compatible_isolation.jl:647
Building CMake ──→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building Blosc ──→ `~/.julia/packages/Blosc/lzFr0/deps/build.log`
Building HDF5 ───→ `~/.julia/packages/HDF5/Zh9on/deps/build.log`
Building GLPK ───→ `~/.julia/packages/GLPK/J1b5G/deps/build.log`
Testing COBRA
Resolving package versions...
Status `/tmp/jl_5qkJs5/Manifest.toml`
[6e4b80f9] BenchmarkTools v0.4.3
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.5.1
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[58298e0b] COBRA v0.3.0
[a076750e] CPLEX v0.6.1
[34da2185] Compat v2.2.0
[60bf3e95] GLPK v0.12.0
[3c7084bd] GLPKMathProgInterface v0.4.4
[f67ccb44] HDF5 v0.12.5
[cd3eb016] HTTP v0.8.8
[83e8ac13] IniFile v0.5.0
[682c06a0] JSON v0.21.0
[2ec943e9] Libz v1.0.0
[23992714] MAT v0.6.0
[b8f27783] MathOptInterface v0.9.7
[fdba3010] MathProgBase v0.7.7
[739be429] MbedTLS v0.7.0
[bac558e1] OrderedCollections v1.1.0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[30578b45] URIParser v0.4.0
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1094
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:432
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
>> Checking the system's configuration ...
GLPKMathProgInterface is installed.
Package Gurobi is not installed. In order to use Gurobi, you must first run `Pkg.add("Gurobi")`
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1094
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:432
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
Package CPLEX is not installed. In order to use CPLEX, you must first run `Pkg.add("CPLEX")`
>> Done. 1 solvers are installed and ready to use.
[ Info: Parallel version - Connecting the 4 workers ...
4 local workers are connected. (+1) on host: 0bd00afa28a5
Downloading the ecoli_core model ...Done.
┌ Warning: The MATLAB package is not present. The tests for PALM.jl will not be run.
└ @ Main ~/.julia/packages/COBRA/fOo2U/test/runtests.jl:97
> Testing GLPKMathProgInterface ... Done.
> Testing CPLEX ... Not supported.
> Testing Gurobi ... Not supported.
-- Running 13 tests using the GLPKMathProgInterface solver. --
Running s_all.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 2.6190478801727295 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_all.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 8.719033002853394
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_core.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0017750263214111328 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_core.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 0.20874500274658203
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_distinct.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0018091201782226562 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (73, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.001795053482055664 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
>> Size of stoichiometric matrix: (74, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.012559175491333008 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Array{Int64,1}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_distinct.jl
Original FBA obj.val 0.8739215069685877
Maximum of maxFlux: 26.528869396061772
Minimum of maxFlux: -9.04660613349818
Maximum of minFlux: 15.206494614374979
Minimum of minFlux: -10.0
Norm of maxFlux: 37.02464689379309
Norm of minFlux: 22.00443371346725
Solution time [s]: 0.1629800796508789
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_fba.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
Original FBA. No additional constraints have been added.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 1.4175691604614258
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0021898746490478516
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0021369457244873047
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0320279598236084
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Int64) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.0
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.0
Norm of minFlux: 0.0
Solution time [s]: 0.013535022735595703
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_tools.jl ...
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: Some reaction names are not in the model; their indices in the `rxnsList` are reported in `rxnIDsNE`.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/tools.jl:88
Running z_all.jl ...
[ Info: The ecoli_core model already exists.
>> The following tests throw warning messages for testing purposes. <<
[ Info: Sequential version - Depending on the model size, expect long execution times.
Loading SSH connection details from /root/.julia/packages/COBRA/fOo2U/src/../config/sshCfg.jl ...Done.
[ Info: Parallel version - Connecting the 56 workers ...
[ Info: Connecting SSH nodes ...
>> Connecting 8 workers on first.last@server1.com
[ Info: Parallel version - Connecting the 4 workers ...
[ Info: Parallel version - Connecting the 2 workers ...
4 workers already connected. No further workers to connect.
2 workers already connected. No further workers to connect.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
┌ Warning: The `rxnsList` has more reactions than in the model. `rxnsList` shorted to the maximum number of reactions.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:637
Original FBA. No additional constraints have been added.
>> Only 96 reactions of 95 will be solved (~ 101.05263157894737 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = min]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865298, norm(fbaSol) = 106.8373155300231.
>> Size of stoichiometric matrix: (73, 95)
No objective set (`c` is zero). objValue and fbaSol not defined. optPercentage = 90.0.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
-- Minimization (iRound = 0). Block 1 [1/2].
[ Info: The model named modelTest loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/testData.mat is a uncoupled model.
-- Maximization (iRound = 1). Block 1 [1/2].
>> Note: Warnings above are thrown for testing purposes and can be safely ignored.
-- All tests passed. --
Testing COBRA tests passed
Results with Julia v1.3.0
Testing was successful.
Last evaluation was ago and took 4 minutes, 37 seconds.
Resolving package versions...
Installed IniFile ─────────────── v0.5.0
Installed URIParser ───────────── v0.4.0
Installed Parsers ─────────────── v0.3.10
Installed Compat ──────────────── v2.2.0
Installed Libz ────────────────── v1.0.0
Installed BinaryProvider ──────── v0.5.8
Installed CPLEX ───────────────── v0.6.1
Installed COBRA ───────────────── v0.3.0
Installed Parameters ──────────── v0.12.0
Installed CMakeWrapper ────────── v0.2.3
Installed BinDeps ─────────────── v0.8.10
Installed MathOptInterface ────── v0.9.7
Installed OrderedCollections ──── v1.1.0
Installed JSON ────────────────── v0.21.0
Installed MbedTLS ─────────────── v0.7.0
Installed MAT ─────────────────── v0.6.0
Installed GLPKMathProgInterface ─ v0.4.4
Installed CMake ───────────────── v1.1.2
Installed Blosc ───────────────── v0.5.1
Installed HDF5 ────────────────── v0.12.5
Installed MathProgBase ────────── v0.7.7
Installed HTTP ────────────────── v0.8.8
Installed GLPK ────────────────── v0.12.0
Installed BenchmarkTools ──────── v0.4.3
Installed BufferedStreams ─────── v1.0.0
Updating `~/.julia/environments/v1.3/Project.toml`
[58298e0b] + COBRA v0.3.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[6e4b80f9] + BenchmarkTools v0.4.3
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[a74b3585] + Blosc v0.5.1
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[58298e0b] + COBRA v0.3.0
[a076750e] + CPLEX v0.6.1
[34da2185] + Compat v2.2.0
[60bf3e95] + GLPK v0.12.0
[3c7084bd] + GLPKMathProgInterface v0.4.4
[f67ccb44] + HDF5 v0.12.5
[cd3eb016] + HTTP v0.8.8
[83e8ac13] + IniFile v0.5.0
[682c06a0] + JSON v0.21.0
[2ec943e9] + Libz v1.0.0
[23992714] + MAT v0.6.0
[b8f27783] + MathOptInterface v0.9.7
[fdba3010] + MathProgBase v0.7.7
[739be429] + MbedTLS v0.7.0
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[30578b45] + URIParser v0.4.0
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CPLEX ──→ `~/.julia/packages/CPLEX/iAQQk/deps/build.log`
┌ Error: Error building `CPLEX`:
│ ERROR: LoadError: Unable to locate CPLEX installation. Note this must be downloaded separately. See the CPLEX.jl README for further instructions.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] try_local_installation() at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:64
│ [3] top-level scope at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:86
│ [4] include at ./boot.jl:328 [inlined]
│ [5] include_relative(::Module, ::String) at ./loading.jl:1105
│ [6] include(::Module, ::String) at ./Base.jl:31
│ [7] include(::String) at ./client.jl:424
│ [8] top-level scope at none:5
│ in expression starting at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:77
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
Building MbedTLS → `~/.julia/packages/MbedTLS/a1JFn/deps/build.log`
Building CMake ──→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building Blosc ──→ `~/.julia/packages/Blosc/lzFr0/deps/build.log`
Building HDF5 ───→ `~/.julia/packages/HDF5/Zh9on/deps/build.log`
Building GLPK ───→ `~/.julia/packages/GLPK/J1b5G/deps/build.log`
Testing COBRA
Resolving package versions...
Status `/tmp/jl_OixSZ5/Manifest.toml`
[6e4b80f9] BenchmarkTools v0.4.3
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.5.1
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[58298e0b] COBRA v0.3.0
[a076750e] CPLEX v0.6.1
[34da2185] Compat v2.2.0
[60bf3e95] GLPK v0.12.0
[3c7084bd] GLPKMathProgInterface v0.4.4
[f67ccb44] HDF5 v0.12.5
[cd3eb016] HTTP v0.8.8
[83e8ac13] IniFile v0.5.0
[682c06a0] JSON v0.21.0
[2ec943e9] Libz v1.0.0
[23992714] MAT v0.6.0
[b8f27783] MathOptInterface v0.9.7
[fdba3010] MathProgBase v0.7.7
[739be429] MbedTLS v0.7.0
[bac558e1] OrderedCollections v1.1.0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[30578b45] URIParser v0.4.0
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:425
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
>> Checking the system's configuration ...
GLPKMathProgInterface is installed.
Package Gurobi is not installed. In order to use Gurobi, you must first run `Pkg.add("Gurobi")`
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:425
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
Package CPLEX is not installed. In order to use CPLEX, you must first run `Pkg.add("CPLEX")`
>> Done. 1 solvers are installed and ready to use.
[ Info: Parallel version - Connecting the 4 workers ...
4 local workers are connected. (+1) on host: fa060208e5b3
Downloading the ecoli_core model ...Done.
┌ Warning: The MATLAB package is not present. The tests for PALM.jl will not be run.
└ @ Main ~/.julia/packages/COBRA/fOo2U/test/runtests.jl:97
> Testing GLPKMathProgInterface ... Done.
> Testing CPLEX ... Not supported.
> Testing Gurobi ... Not supported.
-- Running 13 tests using the GLPKMathProgInterface solver. --
Running s_all.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 2.803959846496582 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_all.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 8.076079845428467
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_core.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0018429756164550781 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_core.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 0.20491504669189453
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_distinct.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0019559860229492188 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (73, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.0016961097717285156 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
>> Size of stoichiometric matrix: (74, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.0016720294952392578 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Array{Int64,1}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_distinct.jl
Original FBA obj.val 0.8739215069685877
Maximum of maxFlux: 26.528869396061772
Minimum of maxFlux: -9.04660613349818
Maximum of minFlux: 15.206494614374979
Minimum of minFlux: -10.0
Norm of maxFlux: 37.02464689379309
Norm of minFlux: 22.00443371346725
Solution time [s]: 0.1931619644165039
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_fba.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 1.6068689823150635
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0020918846130371094
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0023698806762695312
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.038285017013549805
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Int64) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.0
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.0
Norm of minFlux: 0.0
Solution time [s]: 0.0034890174865722656
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_tools.jl ...
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: Some reaction names are not in the model; their indices in the `rxnsList` are reported in `rxnIDsNE`.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/tools.jl:88
Running z_all.jl ...
[ Info: The ecoli_core model already exists.
>> The following tests throw warning messages for testing purposes. <<
[ Info: Sequential version - Depending on the model size, expect long execution times.
Loading SSH connection details from /root/.julia/packages/COBRA/fOo2U/src/../config/sshCfg.jl ...Done.
[ Info: Parallel version - Connecting the 56 workers ...
[ Info: Connecting SSH nodes ...
>> Connecting 8 workers on first.last@server1.com
[ Info: Parallel version - Connecting the 4 workers ...
4 workers already connected. No further workers to connect.
[ Info: Parallel version - Connecting the 2 workers ...
2 workers already connected. No further workers to connect.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
Original FBA. No additional constraints have been added.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
┌ Warning: The `rxnsList` has more reactions than in the model. `rxnsList` shorted to the maximum number of reactions.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:637
>> Only 96 reactions of 95 will be solved (~ 101.05263157894737 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = min]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865298, norm(fbaSol) = 106.8373155300231.
>> Size of stoichiometric matrix: (73, 95)
No objective set (`c` is zero). objValue and fbaSol not defined. optPercentage = 90.0.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
-- Minimization (iRound = 0). Block 1 [1/2].
[ Info: The model named modelTest loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/testData.mat is a uncoupled model.
-- Maximization (iRound = 1). Block 1 [1/2].
>> Note: Warnings above are thrown for testing purposes and can be safely ignored.
-- All tests passed. --
Testing COBRA tests passed
Results with Julia v1.3.1-pre-7704df0a5a
Testing was successful.
Last evaluation was ago and took 4 minutes, 22 seconds.
Resolving package versions...
Installed GLPKMathProgInterface ─ v0.4.4
Installed CMake ───────────────── v1.1.2
Installed Compat ──────────────── v2.2.0
Installed MbedTLS ─────────────── v0.7.0
Installed BenchmarkTools ──────── v0.4.3
Installed HDF5 ────────────────── v0.12.5
Installed BinDeps ─────────────── v0.8.10
Installed COBRA ───────────────── v0.3.0
Installed Blosc ───────────────── v0.5.1
Installed GLPK ────────────────── v0.12.0
Installed BufferedStreams ─────── v1.0.0
Installed CMakeWrapper ────────── v0.2.3
Installed URIParser ───────────── v0.4.0
Installed HTTP ────────────────── v0.8.8
Installed Libz ────────────────── v1.0.0
Installed BinaryProvider ──────── v0.5.8
Installed IniFile ─────────────── v0.5.0
Installed Parameters ──────────── v0.12.0
Installed MathProgBase ────────── v0.7.7
Installed OrderedCollections ──── v1.1.0
Installed MathOptInterface ────── v0.9.7
Installed CPLEX ───────────────── v0.6.1
Installed JSON ────────────────── v0.21.0
Installed Parsers ─────────────── v0.3.10
Installed MAT ─────────────────── v0.6.0
Updating `~/.julia/environments/v1.3/Project.toml`
[58298e0b] + COBRA v0.3.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[6e4b80f9] + BenchmarkTools v0.4.3
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[a74b3585] + Blosc v0.5.1
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[58298e0b] + COBRA v0.3.0
[a076750e] + CPLEX v0.6.1
[34da2185] + Compat v2.2.0
[60bf3e95] + GLPK v0.12.0
[3c7084bd] + GLPKMathProgInterface v0.4.4
[f67ccb44] + HDF5 v0.12.5
[cd3eb016] + HTTP v0.8.8
[83e8ac13] + IniFile v0.5.0
[682c06a0] + JSON v0.21.0
[2ec943e9] + Libz v1.0.0
[23992714] + MAT v0.6.0
[b8f27783] + MathOptInterface v0.9.7
[fdba3010] + MathProgBase v0.7.7
[739be429] + MbedTLS v0.7.0
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[30578b45] + URIParser v0.4.0
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CMake ──→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building Blosc ──→ `~/.julia/packages/Blosc/lzFr0/deps/build.log`
Building HDF5 ───→ `~/.julia/packages/HDF5/Zh9on/deps/build.log`
Building MbedTLS → `~/.julia/packages/MbedTLS/a1JFn/deps/build.log`
Building GLPK ───→ `~/.julia/packages/GLPK/J1b5G/deps/build.log`
Building CPLEX ──→ `~/.julia/packages/CPLEX/iAQQk/deps/build.log`
┌ Error: Error building `CPLEX`:
│ ERROR: LoadError: Unable to locate CPLEX installation. Note this must be downloaded separately. See the CPLEX.jl README for further instructions.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] try_local_installation() at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:64
│ [3] top-level scope at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:86
│ [4] include at ./boot.jl:328 [inlined]
│ [5] include_relative(::Module, ::String) at ./loading.jl:1105
│ [6] include(::Module, ::String) at ./Base.jl:31
│ [7] include(::String) at ./client.jl:424
│ [8] top-level scope at none:5
│ in expression starting at /root/.julia/packages/CPLEX/iAQQk/deps/build.jl:77
└ @ Pkg.Operations /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
Testing COBRA
Resolving package versions...
Status `/tmp/jl_fhDejW/Manifest.toml`
[6e4b80f9] BenchmarkTools v0.4.3
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.5.1
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[58298e0b] COBRA v0.3.0
[a076750e] CPLEX v0.6.1
[34da2185] Compat v2.2.0
[60bf3e95] GLPK v0.12.0
[3c7084bd] GLPKMathProgInterface v0.4.4
[f67ccb44] HDF5 v0.12.5
[cd3eb016] HTTP v0.8.8
[83e8ac13] IniFile v0.5.0
[682c06a0] JSON v0.21.0
[2ec943e9] Libz v1.0.0
[23992714] MAT v0.6.0
[b8f27783] MathOptInterface v0.9.7
[fdba3010] MathProgBase v0.7.7
[739be429] MbedTLS v0.7.0
[bac558e1] OrderedCollections v1.1.0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[30578b45] URIParser v0.4.0
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:425
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
>> Checking the system's configuration ...
GLPKMathProgInterface is installed.
Package Gurobi is not installed. In order to use Gurobi, you must first run `Pkg.add("Gurobi")`
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:13
[3] include at ./boot.jl:328 [inlined]
[4] include_relative(::Module, ::String) at ./loading.jl:1105
[5] include(::Module, ::String) at ./Base.jl:31
[6] top-level scope at none:2
[7] eval at ./boot.jl:330 [inlined]
[8] eval(::Expr) at ./client.jl:425
[9] top-level scope at ./none:3
in expression starting at /root/.julia/packages/CPLEX/iAQQk/src/CPLEX.jl:10
Package CPLEX is not installed. In order to use CPLEX, you must first run `Pkg.add("CPLEX")`
>> Done. 1 solvers are installed and ready to use.
[ Info: Parallel version - Connecting the 4 workers ...
4 local workers are connected. (+1) on host: 63005a436328
Downloading the ecoli_core model ...Done.
┌ Warning: The MATLAB package is not present. The tests for PALM.jl will not be run.
└ @ Main ~/.julia/packages/COBRA/fOo2U/test/runtests.jl:97
> Testing GLPKMathProgInterface ... Done.
> Testing CPLEX ... Not supported.
> Testing Gurobi ... Not supported.
-- Running 13 tests using the GLPKMathProgInterface solver. --
Running s_all.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 2.5187790393829346 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_all.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 7.957953214645386
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_core.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0022809505462646484 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_core.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 0.2109849452972412
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_distinct.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0014929771423339844 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (73, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.0019638538360595703 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
>> Size of stoichiometric matrix: (74, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.0021970272064208984 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Array{Int64,1}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_distinct.jl
Original FBA obj.val 0.8739215069685877
Maximum of maxFlux: 26.528869396061772
Minimum of maxFlux: -9.04660613349818
Maximum of minFlux: 15.206494614374979
Minimum of minFlux: -10.0
Norm of maxFlux: 37.02464689379309
Norm of minFlux: 22.00443371346725
Solution time [s]: 0.1711258888244629
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_fba.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 1.2534599304199219
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0021491050720214844
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.002505064010620117
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0340578556060791
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Int64) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/root/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.0
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.0
Norm of minFlux: 0.0
Solution time [s]: 0.003648042678833008
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_tools.jl ...
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: Some reaction names are not in the model; their indices in the `rxnsList` are reported in `rxnIDsNE`.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/tools.jl:88
Running z_all.jl ...
[ Info: The ecoli_core model already exists.
>> The following tests throw warning messages for testing purposes. <<
[ Info: Sequential version - Depending on the model size, expect long execution times.
Loading SSH connection details from /root/.julia/packages/COBRA/fOo2U/src/../config/sshCfg.jl ...Done.
[ Info: Parallel version - Connecting the 56 workers ...
[ Info: Connecting SSH nodes ...
>> Connecting 8 workers on first.last@server1.com
[ Info: Parallel version - Connecting the 4 workers ...
4 workers already connected. No further workers to connect.
[ Info: Parallel version - Connecting the 2 workers ...
2 workers already connected. No further workers to connect.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
┌ Warning: The `rxnsList` has more reactions than in the model. `rxnsList` shorted to the maximum number of reactions.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:637
Original FBA. No additional constraints have been added.
>> Only 96 reactions of 95 will be solved (~ 101.05263157894737 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = min]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865298, norm(fbaSol) = 106.8373155300231.
>> Size of stoichiometric matrix: (73, 95)
No objective set (`c` is zero). objValue and fbaSol not defined. optPercentage = 90.0.
[ Info: The model named model loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
-- Minimization (iRound = 0). Block 1 [1/2].
[ Info: The model named modelTest loaded from /root/.julia/packages/COBRA/fOo2U/src/../test/testData.mat is a uncoupled model.
-- Maximization (iRound = 1). Block 1 [1/2].
>> Note: Warnings above are thrown for testing purposes and can be safely ignored.
-- All tests passed. --
Testing COBRA tests passed